title: H358-R RMC 48h rep 2


title: Adult HSC WT Rep1

status: Public on Feb 20 2024

type: SRA

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

library_source: transcriptomic

data_processing:
Raw reads quality trimmed using trim_galore with q 30
Mapping to GRCm38 using hisat2
Differential expression analysis with cuffdiff
Gene set enrichment analysis with g:Profiler
Assembly: GRCm38 mouse genome
Supplementary files format and content: tab delimited cuffdiff output files of gene expression

molecule: polyA RNA

organism: Mus musculus

source_name: HSC

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA sequencing libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® kit and NEBNext® Poly(A) mRNA Magnetic Isolation module kit following the manufacturer’s instructions. For hepatocytes, sequencing libraries were prepared using the NEBNext® UltraTM II RNA Library Prep Kit for Illumina® kit following the manufacturer’s instructions. Subsequently, all libraries were ligated to NEBNext® Multiplex Oligos for Illumina® (Dual Index Primer Set I)

tag: strain

tag: cell type

value: HSC

tag: genotype

value: WT


title: H358-R RMC 48h rep 1

city: San Francisco

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

country: USA

institute: University of California, San Franciso

data_processing:
RNA-Seq reads were mapped to the hg19 reference genome using STAR (Spliced Transcripts Align to a Reference, v2.4.2a).
The expression level of transcript per million (TPM) reads were quantified using RNA-Seq by Expectation-Maximization algorithm (RSEM v1.2.29).
The quantified gene expressions of 26,334 transcripts (including coding genes and non-coding genes) were processed in R studio.
Differentially expressed genes between tumor and normal samples were identified using the EdgeR algorithm.
Gene set enrichment analysis was done using GSEA 4.0.1 software.
Assembly: hg19
Supplementary files format and content: Quantified gene expression in TPM for each experimental condition

molecule: total RNA

organism: Homo sapiens

source_name: Lung cancer

extract_protocol:
RNA was extracted from snap-frozen tissue or cell pellets. For tissue samples, tissue was minced using a liquid nitrogen-cooled mortar and pestle before RNA extraction. RNA isolation was performed using the RNeasy Mini kit (Qiagen) including an on-column DNase I digestion. RNA quality was assessed by automated electrophoresis using the RNA 6000 Pico Kit and an Agilent 2100 BioAnalyzer (Agilent Technologies, Inc.). RNA was quantified using the Qubit RNA HS Assay Kit and a Qubit 2.0 fluorometer (Thermo Fisher Scientific).
Library preparation and paired-end 150bp (PE150, Illumina) RNA sequencing was performed by Novogene (Novogene Corporation, Sacramento, USA).

tag: tissue

value: Lung cancer

tag: cell line

value: resistant

tag: treatment


title: Ctrl_12h_10

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:
Read 1 (sample barcodes and unique molecular identifiers) and Read 2 (poly(A) cDNA inserts) were demultiplexed and aligned to the reference genome using STAR with soft clipping enabled, as follows: STAR --runMode alignReads --outSAMmapqUnique 60 --runThreadN 8 --outSAMunmapped Within --soloStrand Forward --quantMode GeneCounts --outBAMsortingThreadN 8 --genomeDir /STAR_Index --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 12 --soloUMIstart 13 --soloUMIlen 9 --soloCellFilter None --soloCBwhitelist barcodefile.txt --soloFeatures Gene --outSAMattributes NH HI nM AS CR UR CB UB GX GN sS sQ sM --outFilterMultimapNmax 1 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outFileNamePrefix bamfiles --readFilesIn R2.fastq.gz R1.fastq.gz
A read-count matrix was assembled utilising BRBseqTools-1.6.jar as follows: java -jar BRBseqTools-1.6.jar ExtractReadCountMatrix -b bamfilesAligned.sortedByCoord.out.bam -c barcodefile_brbseq.txt -gtf star_index/Homo_sapiens.GRCh38.90.gtf -o count_matrix
Processing of raw reads and pair-wise differential gene expression were conducted via EdgeR (version 3.36.0).
Assembly: Ensembl GRCh38, release 90
Supplementary files format and content: Tab-delimited text file containing raw gene-level read-counts across all samples

source_name: SU-DIPG-VI

growth_protocol: Neurosphere cultures were maintained in Tumor Stem Media (TSM) consisting of DMEM/F12 and neurobasal A, supplemented with B27 supplement minus vitamin A, human-bFGF (20 ng/ml), human-EGF (20 ng/ml), human-PGDF-AA (10ng/ml), human-PDGF-BB (10 ng/ml) and heparin (10 ng/ml) at time of use. When confluent, neurospheres were dissociated using Stempro Acctuase for serial culture or use in in vitro assays. No antibiotics were added. Cells maintained at 5% C02 and 37 degrees Celsius.

extract_protocol:
Total RNA was extracted via RNeasy Plus Micro Kit (Qiagen) as per the manufacturer's instructions.
RNA libraries for BRB-seq were prepared via the AlitheaGenomics Mercurius BRB-seq kit for 96 samples (V.0.1.61), as per the manufacturer's instructions.
BRB-seq (Bulk RNA Barcoding Sequencing)

treatment_protocol: Cells were treated with 0.5µM Paxilisib or 1% DMSO for 6 or 12 hours.

value: SU-DIPG-VI

value: Diffuse intrinsic pontine glioma

value: DMSO, 1%

tag: time

value: 12 hours


title: MOUNTSINAI_4

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from mice were mapped to hg38 using HISAT2.
Counts of reads mapping to genes were obtained using htseq-counts software against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files

source_name: Brain

extract_protocol:
To isolate RNA from cultured GBM aggregates, the solid Matrigel was first dissolved by addition of Cultrex Organoid Harvesting Solution (OHS; R&D systems). For each condition, 30 GBM aggregates were taken up with a 1 ml micropipette with cut-off tip from the 96-well U-wells and collected in a 6-well dish, to which 5 ml Cultrex OHS was added for 30 min and placed on a shaker in a 4°C cold room. Aggregates were collected in a 15 ml tube and pelleted by spinning at 1,000 rpm for 5 minutes, then 350 µl RLT buffer of the RNAeasy kit (Qiagen) was added to lyse aggregates by grinding them up with a Doune homogenizer. The lysed RNA in RLT buffer was stored at -80°C until further processing. To prepare cDNA libraries for Illumina sequencing from lysed RNA of GBM aggregates, total RNA was isolated with the RNeasy Micro kit.
The cDNA libraries were synthesized with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina by using100 ng RNA as input for each replicate sample.

value: Brain

value: UCA

value: GBM

value: Hypoxia


title: Ctrl_12h_8


title: MOUNTSINAI_3

value: Normoxia


title: H358 RMC 9d rep 3

value: drug-tolerant persister


title: D2_LPS/IFNγ-Mφ_rep2

city: Anhui

first: Ying

last: Chen

state: China

address: No. 81 Meishan Road, Hefei

country: China

institute: Anhui Medical University

data_processing:
Illumina software used for basecalling.
Sequenced reads with low-quality and adapters were trimmed by Trimmomatic-0.39 softeware, then mapped to mm10 whole genome using STAR-2.7.2b with defalt parameters
The unique reads were used to calculate the fragments per kilobase of exon per million fragments mapped (FPKM) with Cufflinks-2.2.1.
Find differential expression genes between stages, HOMER software command getDiffExpression.pl with DESeq2 was employed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: RAW264.7 cell line

growth_protocol: cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FCS).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW264.7 cells were stimulated for 24 h with lipopolysaccharide (LPS, 50 ng/ml, Sigma) and IFN-γ (20 ng/ml), namely LPS/IFNγ-Mφ.

value: mouse leukemia cell of monocyte macrophage

value: LPS/IFNγ-Mφ


title: Ctrl_12h_7


title: MOUNTSINAI_2


title: H358 RMC 9d rep 2


title: Ctrl_12h_6


title: C3_TgMIF-Mφ_rep3

value: TgMIF-Mφ


title: MOUNTSINAI_1


title: D1_LPS/IFNγ-Mφ_rep1


title: Adult HSC WT Rep3

value: HSC


title: H358 RMC 9d rep 1


title: Ctrl_12h_5


title: C2_TgMIF-Mφ_rep2


title: H358 RMC 48h rep 3

value: acute


title: C1_TgMIF-Mφ_rep1


title: Ctrl_12h_3


title: Ctrl_12h_9


title: B2_LV-Mφ_rep2

value: LV-Mφ


title: NAAP_22

city: Vancouver

first: Robert

middle: E. W.

last: Hancock

state: British Columbia

address: 2259 - Lower Mall Research Station

department: Department of Microbiology & Immunology

country: Canada

institute: University of British Columbia

description:
204
count_matrix.csv

data_processing:
Read alignment to reference using STAR v2.6.9c and default parameters.
Total counts of reads mapping to genes compiled using HTSeq v0.9.1 with stranded mode set to reverse and minimum quality 10.
Globin genes and low count genes (less than 10 counts in 24 or more samples) were removed from count matrix.
Assembly: Ensembl GRCh 38.92
Supplementary files format and content: .Count files have summarized counts per gene
Supplementary files format and content: count_matrix.csv is a comma-separated file summarizing the counts of each gene (rows) in each sample (columns).

source_name: Peripheral whole blood

growth_protocol: 3mL of whole blood was collected from patients directly into Tempus Blood RNA tubes (Applied Biosystems)

extract_protocol:
Total RNA was extracted using Tempus Spin RNA isolation reagent kit (Applied Biosystems). Poly-A RNA was enriched using the NEBNext Poly(A) mRNA magnetic isolation module (NEB).
Strand-specific cDNA libraries were generated using KAPA RNA HyperPrep Kit (Roche).

value: Peripheral whole blood

tag: disease category

value: Non-appendicitis abdominal pain (NAAP)


title: NAAP_21

description:
201
count_matrix.csv


title: H358 RMC 48h rep 2

value: Lung cancer


title: NAAP_20

description:
199
count_matrix.csv


title: NAAP_19

description:
197
count_matrix.csv


title: B1_LV-Mφ_rep1


title: Ctrl_12h_2

value: SU-DIPG-VI

value: Diffuse intrinsic pontine glioma

value: DMSO, 1%


title: A2_Mφ_rep2

value: Mφ


title: H358 ctrl 48h rep 3

value: parental

value: untreated 0.1% DMSO


title: Ctrl_12h_1

value: 12 hours


title: NAAP_18

description:
196
count_matrix.csv


title: H358 ctrl 48h rep 2


title: A1_Mφ_rep1


title: NAAP_17

description:
195
count_matrix.csv


title: Ctrl_6h_6

value: 6 hours


title: H358 RMC 48h rep 1


title: Ctrl_6h_5


title: H358 ctrl 48h rep 1


title: Old_mouse_brain_D1-2

city: Guangzhou

first: Cheng

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

description: Visium Spatial Gene Expression

data_processing:
Illumina BCL files were converted to fastq files by using 10X Genomics Space Ranger pipeline spaceranger mkfastq function (https://support.10xgenomics.com/).
Fastq files were aligned to mm10 reference, manually aligned to respective H&E stain images using spaceranger count (spaceranger v 1.2.0) to obtain the spatial transcription profiles.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw and fittered gene-cell counts for every sample, tissue hires image, tissue position list, scale factors and Hematoxylin & H&E stain images

extract_protocol:
Young (2 months old) and old mice (28 months old) (strain C57BL/6J) were euthanized with an overdose of isoflurane. The brains were rapidly extracted from the cranial cavity, and immediately submerged in ice-cold artificial cerebrospinal fluid. The brains were then blotted to remove excess liquid and were subsequently embedded in optimal cutting temperature (OCT) compound (SAKURA). The brains with OCT compound were quick-frozen on dry ice immediately and stored at -80℃ until cryosectioning process. The cryosectioning placed in a cryostat (Leica, CM1950) to cryosection the OCT embedded tissue blocks into appropriately sized sections for Visium Spatial slides while keeping the samples frozen. Brain sections were 10 μm thick each
10x Genomics Visium Spatial protocols
Spatial scRNA-seq

value: Brain tissue

tag: age

value: Old

tag: region

value: cerebrum, brain stem and fiber tracts


title: Ctrl_12h_4


title: Old_mouse_brain_C1-2

description: Visium Spatial Gene Expression


title: Ctrl_6h_4


title: H3122-R Alec 48h rep 3

value: resistant

value: Alectinib 500 nM 48h


title: Ctrl_6h_3


title: NAAP_15

description:
188
count_matrix.csv


title: NAAP_14

description:
187
count_matrix.csv


title: Ctrl_6h_2


title: H3122-R Alec 48h rep 1


title: NAAP_13

description:
186
count_matrix.csv


title: H3122-R Alec 48h rep 2


title: Old_mouse_brain_A1-2

description: Visium Spatial Gene Expression


title: Old_mouse_brain_B1-2

description: Visium Spatial Gene Expression


title: Young_mouse_brain_D1-1

description: Visium Spatial Gene Expression

value: Young


title: H3122 Alec 9d rep 3

value: drug-tolerant persister

value: Alectinib 500 nM 18d


title: H3122 Alec 9d rep 2

value: Lung cancer


title: Ctrl_6h_1

value: SU-DIPG-VI


title: Young_mouse_brain_C1-1

description: Visium Spatial Gene Expression


title: NAAP_12

description:
179
count_matrix.csv

value: Peripheral whole blood

value: Non-appendicitis abdominal pain (NAAP)


title: Young_mouse_brain_B1-1

description: Visium Spatial Gene Expression


title: NAAP_10

description:
176
count_matrix.csv


title: H3122 Alec 48h rep 3

value: acute


title: NAAP_11

description:
177
count_matrix.csv


title: NAAP_16

description:
191
count_matrix.csv


title: H3122 Alec 9d rep 1


title: Gtl2-polyA-KI_placenta_PKI_miRNA

city: Harbin

first: Ximeijia

last: Zhang

address: 92 Xidazhi Street

institute: Harbin Institute of technology

description: PKI

data_processing:
All reads were aligned to mouse GRCm38/mm10 genome using HISAT2, and genes were counted using StringTie. For miRNA, the mapped reads were aligned with miRbase.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: placenta

extract_protocol:
Total RNA was isolated from E12.5 placentas by using RNAiso (TakaRa) and was treated with DNase I (Thermo Scientific) to remove genomic DNA. Recombinant RNase Inhibitor (TakaRa) was used to protect RNA from degradation. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using RNA-seq library prep kit following the manufacture protocols.

value: placenta

value: PKI

value: paternally Gtl2 polyA knock-in


title: Gtl2-polyA-KI_placenta_HOMO_miRNA

description: HOMO

value: HOMO

value: homozygous


title: Gtl2-polyA-KI_placenta_MKI_miRNA

description: MKI

value: MKI

value: maternally Gtl2 polyA knock-in


title: Young_mouse_brain_A1-1

description: Visium Spatial Gene Expression

value: Brain tissue

value: cerebrum, brain stem and fiber tracts


title: H3122 Alec 48h rep 2

value: Alectinib 500 nM 48h


title: NAAP_8

description:
156
count_matrix.csv


title: Gtl2-polyA-KI_placenta_HOMO_mRNA

description: HOMO


title: H3122 Alec 48h rep 1


title: NAAP_7

description:
155
count_matrix.csv


title: FGK45_5

city: Changchun

first: Cong

last: Fu

state: Jilin

address: NO.17  Xinmin Street

institute: The First Hospital of Jilin University

description: tumor-bearing mice injected with FGK45.5

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to the reference mouse genome (version GRCm38) using HISAT2 (version 2.0.5)
expression levels were calculated as Fragments per Kilobase of transcript per Million reads(FPKM) using StringTie (version 1.3.3b)
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: draining lymph nodes

extract_protocol:
Draining lymph nodes were removed and CD19+ B cells were sorted and collected by FACS. Flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

tag: group

value: tumor-bearing


title: H3122 ctrl 48h rep 3

value: parental

value: untreated 0.1% DMSO


title: Rat_IgG

description: tumor-bearing mice injected with Rat IgG

value: Rat IgG


title: Gtl2-polyA-KI_placenta_MKI_mRNA

description: MKI


title: H3122 ctrl 48h rep 2

value: Lung cancer


title: Gtl2-polyA-KI_placenta_PKI_mRNA

description: PKI


title: GSK3787_FGK45_5

description: tumor-bearing mice injected with GSK3787 and FGK45.5

value: GSK3787 and FGK45.5


title: NAAP_5

description:
146
count_matrix.csv

value: Peripheral whole blood

value: Non-appendicitis abdominal pain (NAAP)


title: Gtl2-polyA-KI_placenta_WT_mRNA

description: WT

value: placenta

value: WT

value: wild type


title: PC9-R Osim 48h rep 3

value: resistant

value: Osimertinib 2 uM 48h


title: NAAP_9

description:
174
count_matrix.csv


title: NAAP_4

description:
140
count_matrix.csv


title: JKD6009 ∆vigR pRAB11::MS2 replicate 2

city: Sydney

first: Jai

middle: Justin

last: Tree

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

description: RNA was prepared from samples using the MAPS protcol (PMID: 25891076)

data_processing:
FASTQ files were mapped and reads depth counted using the CRAC_pipeline_PE.py available at https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines
From the CRAC_pipeline_PE output, the mapped reads in GTF format that have neeb collapsed into blocks and reads with mutations removed ("blocks_nomuts") were converted to BED format using pyGTF2bed.py int eh pyCRAC suite (Webb et al., 2014; PMID: 24393166).
BED formatted files were used as input for the peak calling software BLOCKBUSTER (PMID: 19584066; https://www.bioinf.uni-leipzig.de/~david/LIFE/LIFE/blockbuster.html)
Peak height was calculated using HTSeq (PMID: 25260700)
Statistically signficant peaks (sites enriched in the test condition relative to controls) was determined using DESeq2 (PMID: 25516281)
Assembly: GCF_900607245.1
Supplementary files format and content: BED format fies, read depth in graph format for each sample. These files are the output of CRAC_pipeline_PE and pyGTF2bed. They are input for peak calling with blockbuster, HTSeq, and DESeq2
Supplementary files format and content: final_peaks.csv. This file contains the output from DEseq2. The table is all peaks that have an adjusted p-value of <0.1 and an increase in signal in the test condition. Each peak is labelled with a unique idnetifier in column 1 starting with "clip_peak"
Supplementary files format and content: final_peaks_overlap_features.gff. Peaks that are signficantly enriched in the test condition (from final_peaks.csv) were intersected with genomic features in GFF file for GCF_900607245.1. The output GFF file can be referenced against the DESeq2 DE expression data using the unique peak idnentifier "clip_peak_" in column 9.

organism: Staphylococcus aureus

source_name: whole cell lysate

growth_protocol: Strains were grown in BHI media supplemented with 15 ug/mL chloramphenicol at 37C with 180 rpm shaking to an OD600nm 3.0. Constructs were then induced with 0.4 uM ATc and grown for a further 15 min at 37oC with shaking

extract_protocol: As per MAPS protocol (PMID: 25891076)

treatment_protocol: Test and control strains have an MS2-vigR3'UTR fusion or MS2 alone, respectively.

value: whole cell lysate

value: bacterial cell

value: deltavigR3'UTR pRAB11::MS2


title: WT_H3K27me3_ChIP

city: Pasadena

first: Jimmy

middle: K

last: Guo

address: 1200 E California Blvd

institute: Caltech

library_source: genomic

data_processing:
Paired-end DNA sequencing reads were aligned to the appropriate reference genome (mm9 for mouse and hg19 for human) using Bowtie2 v2.3.1 with the default parameters and with the following deviations. We used a local alignment search (--local) and disabled searching for discordant alignments (--no-discordant).
Assembly: mm9, hg19
Supplementary files format and content: bigwig files were generated at 50nt bins using deepTools

molecule: genomic DNA

extract_protocol:
Mouse embryonic stem cell lines (pSM33) were crosslinked in either 1% formaldehyde or 1% formaldehyde and 2 mM DSG (Thermo #2059). Briefly, cells were washed with room temperature 1X PBS and then incubated in crosslinker solution in PBS at room temperature with gentle rocking for 45 minutes. Cells were then washed with room temperature 1X PBS. After washing, a 1% formaldehyde solution was then added on top of cells and further incubated at room temperature for 10 minutes. To quench the formaldehyde crosslinking, 2 mL of a 2.5M Glycine solution was added to each plate and incubated for an additional 5 minutes. After quenching, cells were washed three times in 1X cold PBS. After the last wash, 7.5 mL of scraping buffer (1X PBS + 0.5% BSA) was added to cells. Cells were then scraped using a rubber policeman, aliquoted into 10 million cell aliquots, and flash frozen until ChIP was performed.
To solubilize chromatin and fragment DNA, cells were lysed and then sonicated. To begin nuclear fractionation, cells were resuspended in 1 mL of Gagnon HLB Buffer + 1X PIC and incubated on ice for 10 minutes. Samples were briefly vortexed and centrifuged at 1250g for 3 minutes at 4°C. Samples were then resuspended in 600 μL of mammalian lysis buffer (1% TritonX-100, 0.1% sodium deoxycholate, 0.1% SDS, 150mM NaCl, and 50mM HEPES pH 7.5) + PIC and transferred to 15 mL Diagenode conical tubes. Following transfer, cells were sonicated using a Bioruptor waterbath sonicator (in 15 mL tubes with adapters) at max intensity for 30 seconds, followed by either 30 seconds of rest for 27 cycles (1% formaldehyde samples) or 30 seconds of rest for 36 cycles (1% formaldehyde + DSG samples). Samples were then transferred to 1.5 mL tubes and cleared of insoluble material by pelleting at 13000 rpm for 10 minutes at 4°C. Supernatants were mixed with 1800 μL HBSS (Thermo Scientific) + 1X PIC and 2400 μL 2X RIPA + 1X PIC. Lysate was incubated overnight with Invitrogen M-280 Sheep Anti-Rabbit IgG Dynabeads coupled with 5 μg of H3K27me3 antibody (Active Motif, 39155) or 5 μg of Goat anti-V5 antibody (Bethyl, A190-119A). Samples were washed with 1 mL of low salt buffer, high salt buffer, LiCl wash buffer, and finally TE buffers. Samples were reverse-crosslinked and Proteinase K-digested overnight at 65°C, and DNA was subsequently purified with Zymo Clean and Concentrate.  Post reverse-crosslinking ChIP libraries were constructed as previously described. Briefly, purified DNA was end repaired and dA-tailed using 1X NEBNext Ultra II End Repair/dA-Tailing Module (NEB, E7546L). DNA adaptors were then ligated to each sample and cleaned up using 0.7X SPRI (AMPure XP) followed by a repeat clean-up with 1X SPRI. PCR amplification was achieved using primers that add the indexed full Illumina adaptor sequences.

value: Mouse embryonic stem cells

tag: chip antibody

value: Cat #39155 from Abcam


title: NAAP_3

description:
126
count_matrix.csv


title: Naïve

description: naïve mice

source_name: lymph nodes in the same site

value: naive mice


title: Gtl2-polyA-KI_placenta_WT_miRNA

description: WT


title: PC9-R Osim 48h rep 2


title: SpyYY1_ChIP

value: Cat #A190-119Afrom Bethyl


title: NAAP_2

description:
125
count_matrix.csv


title: SpySuz12_H3K27me3_ChIP


title: JKD6009 ∆vigR pRAB11::MS2-vigR3UTR replicate 2

value: deltavigR3'UTR pRAB11::MS2-vigR3'UTR


title: PC9 Osim 9d rep 3

value: Lung cancer

value: drug-tolerant persister

value: Osimertinib 2 uM 9d


title: NAAP_6

description:
154
count_matrix.csv

value: Peripheral whole blood

value: Non-appendicitis abdominal pain (NAAP)


title: PC9-R Osim 48h rep 1


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 -Dox biol_rep5

city: Planegg

first: Wolfgang

last: Enard

address: Großhadernerstr. 2

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_10
BC:  TGCCGGATGCTA

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.

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: JKD6009 ∆vigR pRAB11::MS2-vigR3UTR replicate 1


title: PC9 Osim 9d rep 2


title: SpyEzh2_Input

data_processing:
Single-end DNA sequencing reads were aligned to the mm9 reference genome using Bowtie2 v2.3.1 with the default parameters and with the following deviations. We used a local alignment search (--local) and disabled searching for discordant alignments (--no-discordant).
Assembly: mm9, hg19
Supplementary files format and content: bigwig files were generated at 50nt bins using deepTools


title: NAAP_1

description:
119
count_matrix.csv


title: SpySUZ12_ChIP


title: PA_13

description:
158
count_matrix.csv

value: Perforated appendicitis (PA)


title: H3122 ctrl 48h rep 1

value: parental

value: untreated 0.1% DMSO


title: PC9 Osim 9d rep 1


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 -Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_9
BC:  GTCGGCCGATAT


title: SpyEzh2_H3K27me3_ChIP


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 -Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_8
BC:  GGAACAGACCGT


title: JKD6009 ∆vigR pRAB11::MS2 replicate 1

value: whole cell lysate

value: bacterial cell

value: deltavigR3'UTR pRAB11::MS2


title: PC9 Osim 48h rep 3

value: acute

value: Osimertinib 2 uM 48h


title: PA_12

description:
147
count_matrix.csv


title: PC9 Osim 48h rep 2


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 -Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_6
BC:  AGGACATTGGTA


title: PA_11

description:
121
count_matrix.csv


title: SpyEed_H3K27me3_ChIP

value: Mouse embryonic stem cells

value: Cat #39155 from Abcam


title: PA_10

description:
118
count_matrix.csv


title: PA_14

description:
175
count_matrix.csv


title: PC9 Osim 48h rep 1

value: Lung cancer


title: SpyEED_ChIP

value: Cat #A190-119Afrom Bethyl


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 +Dox biol_rep5

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_5
BC:  CACCGTGGATCA

value: +Dox


title: SpyYY1_CLAP

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8. Read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to a combined genome reference containing the mouse (mm10) and human (hg38) genomes using STAR aligner181. PCR duplicates were removed using the Picard MarkDuplicates function. For mixing experiments, only reads that mapped uniquely in the genome and unambiguously to the human or mouse genomes were kept for further analysis. For experiments done in a single species, the appropriate reference genome and alignments were used (mm10 for mouse and hg38 for human). These reads were then used for downstream analysis.  For computing enrichments, all human (hg38) and mouse (mm10) annotated genes (RefSeq, downloaded from UCSC GRCh38 and GRCm38, respectively) were used as a reference set except for the genes encoding the transfected proteins. We treated exonic regions and intronic regions of each annotated gene as separate reference genes for computing enrichment. For each reference gene, we enumerated 100 nucleotide windows that span across the gene; for each window, we calculated: (i) the number of reads overlapping the window in the protein elution sample (e.g., CLIP or CLAP) and (ii) the maximum of either the number of observed reads over the window or the median read count over all windows within the gene in the input sample. Because all windows overlapping a gene should have the same expression level in the input sample, this approach provides a conservative estimation of the input coverage because it prevents windows from being scored as enriched if the input values over a given window are artificially low due to stochastic fluctuation, while at the same time accounting for any non-random issues that lead to increases in read counts over a given window (i.e., alignment artifacts leading to non-random assignment or pileups).  To directly compare the number of reads within each window between sample and input, we normalized each window count by the total number of reads sequenced and the overall complexity within each sample. For example, if one sample was sequenced twice as deeply as another, then we would expect to observe – on average – twice as many reads over a given window for that sample. To account for the differences in the number of mapped (aligned) reads between samples, we scaled the total number of sequenced reads by the proportion of aligned reads within each sample.  For each window, we computed enrichment by dividing the normalized sample counts by the normalized input counts. Nominal p-values were calculated for each window using a binomial test where k (number of successes) is defined as the number of reads in the protein elution samples within the window, N (number of trials) is the sum of the number of reads in the protein elution and input samples, and p (probability of success) is the expected number of reads in the elution sample divided by the sum of the expected number of reads per window in elution and input samples. (The expected number of reads is defined as the total number of reads scaled by the proportion of aligned reads within each sample). For plotting and reporting purposes, we considered all regions with a nominal binomial p-value < 10-6 as significant. However, the overall results reported are robust to the precise p-value cutoff used.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes gene window enrichment calculations
Supplementary files format and content: bedgraph
Library strategy: CLAP-seq

extract_protocol:
Cells were washed once with PBS and then crosslinked on ice using 0.25 J cm-2 (UV 2.5k) of UV at 254 nm in a Spectrolinker UV Crosslinker. Cells were then scraped from culture dishes, washed once with PBS, pelleted by centrifugation at 1500g for 4 min, and flash-frozen in liquid nitrogen for storage at -80 °C.
Cells were lysed in 1 mL lysis buffer (50mM Tris pH 7.5, 100mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 1X Promega PIC). For CLIP samples, RNA was digested with Ambion RNase I (1:3,000 dilution) to achieve a size range of 100-500 nucleotides in length. We used a fixed RNase condition for all experiments to enable comparison between proteins. Lysates were precleared by mixing with Protein G beads (Dynabeads) for 30 minutes at 4°C. Target proteins were immunoprecipitated overnight at 4°C from 10 million cells with 5 μg of antibody coupled to 40 μL of Protein G beads in 100 μL lysis buffer. Antibodies were pre-coupled to beads for 1 hour at room temperature with mixing, followed by 3 washes with lysis buffer to remove unbound protein. After immunoprecipitation, beads were washed four times with high salt wash buffer (50 mM TrisHCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and four times with wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20). RNA and protein were eluted by incubating in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsacrosine, 2.5 mM TCEP) supplemented with 100 mM DTT at 50°C for 20 minutes. Samples were then run through an SDS-PAGE gel and transferred to a nitrocellulose membrane using the iBlot transfer system. The region 70 kDa above the molecular weight of the protein of interest was isolated and treated with Proteinase K (NEB), followed by purification with RNA Clean & Concentrate-5 (Zymo). Anti-V5 antibody (Bethyl, A190-120A) was used for all CLIP experiments.  For CLAP samples, cells were resuspended in 1 mL of cold lysis buffer (50 mM HEPES pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with 1X Protease Inhibitor Cocktail (Promega), 200 U of RiboLock (NEB), 20 U of TURBO DNase (Ambion), and 1X manganese/calcium mix (0.5mM CaCl2, 2.5 mM MnCl2). Samples were incubated on ice for 10 minutes and then at 37°C for 10 minutes at 1150 rpm shaking on a ThermoMixer (Eppendorf). Lysates were cleared by centrifugation at 15000g for 2 minutes and the supernatant was collected for capture to HaloLink Resin (Promega). For each CLAP capture, 200 μL of 25% HaloLink Resin (50 μL of HaloLink Resin total) was used per 10 million cells. Resin was washed three times with 2 mL of 1X TBS (50 mM Tris pH 7.5, 150 mM NaCl) and incubated in 1X Blocking Buffer (50 mM HEPES, pH 7.5, 10 μg/mL Random 9-mer, 100 μg/mL BSA) for 20 minutes at room temperature with continuous rotation. After the incubation, resin was washed three times with 1X TBS. Cleared lysate was mixed with 50 μL of HaloLink Resin and incubated at 4°C overnight with continuous rotation. The captured protein bound to resin was washed three times with lysis buffer at room temperature and then three times at 90°C for 3 minutes while shaking at 1200 rpm with each of the following buffers: 1X ProK/NLS buffer (50 mM HEPES, pH 7.5, 2% NLS, 10 mM EDTA, 0.1% NP-40, 10 mM DTT), high salt buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 1M NaCl), 8M urea buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 8 M Urea), and Tween buffer (50 mM HEPES, pH 7.5, 0.1% Tween 20, 10 mM EDTA). After the last wash, samples were centrifuged at 7500g for 30 seconds and supernatant was discarded. For elution, HaloLink Resin was resuspended in 100 μL of ProK/NLS buffer + 10 μL of Proteinase K (NEB) and incubated at 50°C for 20 minutes while shaking at 1200 rpm. Elutions were then transferred to microspin cups (Pierce, Thermo Fisher), centrifuged at 2000g for 30 seconds, and purified with RNA Clean and Concentrate-5 (Zymo).


title: PA_7

description:
77
count_matrix.csv

value: Peripheral whole blood


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 -Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_7
BC:  CTTCTCGCTACA

value: KRAB-dCas9 iPSCs


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 +Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_3
BC:  CCTCTATGGTCC

value: iPSCs


title: SpySUZ12_CLAP


title: PC9 ctrl 48h rep 1


title: PC9 ctrl 48h rep 2


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 +Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_2
BC:  CCACTCTAGGCT


title: PC9 ctrl 48h rep 3


title: SpyPTBP1_CLAP


title: SpyEZH2_CLAP


title: SpyEZH2_ChIP


title: PA_5

description:
70
count_matrix.csv


title: PA_9

description:
95
count_matrix.csv


title: KN473 cell line, NEO2734 72h, rep2

city: Bordeaux

first: Amandine

last: Crombe

address: 229 cours de l'Argonne

country: France

institute: Institut Bergonié

data_processing:
raw RNAseq sequences were controlled for quality using a set of published tools to produce curated reads
Transcript count data were normalized according the VOOM method and the RNAseq differential gene expression between groups of samples was performed using the statistical t-test from the R package LIMMA
We defined the significantly up- or down-regulated transcripts using an FDR threshold of 0.05. The fold-change used to further filter the differential gene expression was set to a minimum value of 2
For the gene set enrichment analysis, MSigDB and FGSEA were used to identify pathways or gene ontologies in which the genes of an identified group were enriched.
Assembly: hg19
Supplementary files format and content: tab-delimited text file of raw counts matrix
Supplementary files format and content: tab delimited text file of diffenrential expression results

growth_protocol: UPS cells were maintained in RPMI medium 1640 GlutaMAX Supplement in the presence of 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
RNA was extracted using an RNeasy Plus Mini Kit (Qiagen). The purity and concentration of the isolated RNA were determined with a NanoDrop spectrophotometer, and capillary electrophoresis using a Bioanalyzer 2100 was carried out to determine the RNA integrity number (RIN).
RNA libraries were prepared using NEBNext® Ultra™ II mRNA-Seq library kit paired-end 100x2 read protocol
RNA-seq, Number of paired-end reads produced by the sequencer was at least 30M per sample

treatment_protocol: UPS cells were untreated or treated with NEO2734 at the IC50 for IB106/JR588 and at 25µM for IB119/KN473 for 72h

value: UPS (undifferentiated pleomorphic sarcoma)

value: WT


title: PA_4

description:
63
count_matrix.csv

value: Perforated appendicitis (PA)


title: SpyEED_CLAP


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 -Dox biol_rep5

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_10
BC:  AGCATAGCCACA

value: -Dox


title: KN473 cell line, NEO2734 72h, rep1


title: Merged_PSM33_Input


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 -Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_9
BC:  CCTTGACTGTGG


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 +Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_4
BC:  TCTGCGAGATGG


title: PA_3

description:
57
count_matrix.csv


title: PA_8

description:
83
count_matrix.csv


title: KN473 cell line, Control, rep3

value: vehicle


title: coculture EpCAM- Rep2

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

description: coculture EpCAM-

data_processing:
FastQC was used for the quality control of raw sequencing data.
After quality control, Cutadapt was used to remove the low-quality bases and adaptor contaminations. The quality of yield clean data was examined by FastQC software again.
Hisat2 was used to align the clean data to mouse reference genome mm10 which we downloaded from Illumina iGenomes database.
Samtools was used to manipulate SAM files and BAM files. Next, HTSeq-count from HTSeq package was used to count the number of reads that were aligned to the gene features.
The differentially expressed genes were identified by edgeR with cutoff of |log(fold change)| > 1 and p value < 0.01. GSEA analysis was performed by GSEA software with standard genesets from MSigDB database. The visualization of GSEA results was performed by Rtoolbox from https://github.com/PeeperLab/Rtoolbox.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the FPKM normalized gene expression value in each sample.

source_name: Mca-P1362 breast tumor

growth_protocol: All cells were grown in high glucose DMEM medium containing 10% fetal bovine serum and were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol:
RNA extraction and library construction was performed by Admera Health (South Plainfield, NJ).
Illumina HiSeq sequencing platform was employed for the sequencing with the 150bp paired-end mode.

treatment_protocol: EpCAM+ and EpCAM-cells from MCa-P1362 culture were sorted at the Massachusetts General Hospital Flow Cytometry Core. Respective EpCAM- and EpCAM+ cells were either pelleted and immediately flash frozen after sorting or grown at 37°C/5% CO2 in a incubator and passaged once before pelleting and flash freezing.

value: Mca-P1362 breast tumor

value: Mouse breast cancer cells


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 -Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_8
BC:  GTCACCAAGCCA


title: PA_2

description:
52
count_matrix.csv


title: KN473 cell line, Control, rep2


title: coculture EpCAM+ Rep2

description: coculture EpCAM+


title: KN473 cell line, NEO2734 72h, rep3


title: PA_1

description:
46
count_matrix.csv


title: KN473 cell line, Control, rep1


title: coculture EpCAM- Rep1

description: coculture EpCAM-


title: PA_6

description:
74
count_matrix.csv


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 -Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_7
BC:  GACAAGAGCTTA


title: SOX2 knockdown bulk RNA-seq H.i2_clone2 +Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone2_1
BC:  CTTCCTTGTCGG


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 -Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_6
BC:  CTTGGTGGTTCC


title: IB119 cell line, NEO2734 72h, rep3


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 +Dox biol_rep5

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_5
BC:  CCAGTGTCCTTG


title: IB119 cell line, NEO2734 72h, rep2


title: coculture EpCAM+ Rep1

description: coculture EpCAM+


title: SA_35

description:
198
count_matrix.csv

value: Simple appendicitis (SA)


title: SA_34

description:
193
count_matrix.csv


title: monoculture EpCAM- Rep2

description: monoculture EpCAM-


title: SA_33

description:
189
count_matrix.csv


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 +Dox biol_rep4

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_4
BC:  CCTAACCTACAA


title: IB119 cell line, NEO2734 72h, rep1


title: SA_32

description:
185
count_matrix.csv


title: monoculture EpCAM- Rep1

description: monoculture EpCAM-


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 +Dox biol_rep3

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_3
BC:  CCACGTAAGAGG


title: IB119 cell line, Control, rep3


title: monoculture EpCAM+ Rep2

description: monoculture EpCAM+


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 +Dox biol_rep1

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_1
BC:  AGCGATTCCTAA


title: SA_30

description:
181
count_matrix.csv


title: monoculture EpCAM+ Rep1

description: monoculture EpCAM+


title: SA_31

description:
182
count_matrix.csv


title: SOX2 knockdown bulk RNA-seq H.i2_clone1 +Dox biol_rep2

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i2_clone1_2
BC:  GAGTGTCATGTT


title: SA_29

description:
180
count_matrix.csv


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_7
BC:  CGACGTGGCATT


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_8
BC:  TAGCGGTCTGCA


title: AHRmko-34

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

data_processing:
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 Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences
Assembly: Mus musculus GRCm38 reference genome

source_name: gastrocnemius muscle

extract_protocol: Total RNA extracted using Zymo Research DirectZol RNA miniprep kit

treatment_protocol: Four weeks following the last intraperitoneal injection of tamoxifen, AHRmko mice were exposed to either room air or tobacco smoke (TS) for 16 weeks, with TS exposures as described previously [8, 37]. Briefly, 3R4F research-grade cigarettes were purchased from the University of Kentucky (Lexington, KY, USA) and smoked according to the protocol approved by the Federal Trade Commission (1 puff per minute per cigarette, where each puff was 2 s in duration and 35 ml in volume) using a Teague TE-10 smoke exposure system (Teague Enterprises, Woodland, CA, USA). Mice in the TS group were exposed for 1 h, twice per day, 5 days per week for a total of 16 weeks. The concentration of TS was measured during each smoke exposure using a standard flow meter and a filter paper per manufacturer protocol. The average TS concentration across the 16 weeks was 220±80mg/m3. Mice in the air-exposed group were kept in the same barrier facility as the TS-exposed mice, but not exposed to TS.

value: gastrocnemius muscle

tag: strain background

value: AHR-muscle knockout

value: 16 weeks chronic cigarette smoke exposure


title: JR588 cell line, NEO2734 72h, rep2


title: IB119 cell line, Control, rep1


title: JR588 cell line, NEO2734 72h, rep3


title: AHRmko-22


title: SA_28

description:
172
count_matrix.csv


title: JR588 cell line, NEO2734 72h, rep1


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_6
BC:  CTGAAGATACTG


title: AHRmko-19


title: AHRmko-9


title: SA_26

description:
151
count_matrix.csv


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_5
BC:  TCACGCGGATTC


title: AHRmko-8


title: SA_25

description:
149
count_matrix.csv


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_4
BC:  GATAGCTGCGAA


title: AHRfl-33

value: AHR-floxed


title: JR588 cell line, Control, rep2


title: SA_24

description:
143
count_matrix.csv


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_3
BC:  GTGCCATAAGAA


title: IB119 cell line, Control, rep2


title: JR588 cell line, Control, rep1


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_2
BC:  ATTCGAATTCCG


title: SA_23

description:
142
count_matrix.csv


title: IB106 cell line, NEO2734 72h, rep3


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

description:
sample_annotation_data_submission.xlsx
Sox2_human.dgecounts.rds
SOX2_KD_bulkRNA-seq_H.i1_clone1_1
BC:  CTTCCAGAGGCA


title: SA_27

description:
162
count_matrix.csv


title: IB106 cell line, NEO2734 72h, rep2


title: IB106 cell line, NEO2734 72h, rep1


title: AHRfl-12


title: SA_22

description:
132
count_matrix.csv


title: SA_21

description:
131
count_matrix.csv


title: SA_20

description:
120
count_matrix.csv


title: AHRfl-11


title: IB106 cell line, Control, rep3


title: JR588 cell line, Control, rep3


title: IB106 cell line, Control, rep2


title: SA_19

description:
116
count_matrix.csv


title: IB106 cell line, Control, rep1


title: SA_18

description:
112
count_matrix.csv


title: AHRfl-15


title: SA_17

description:
111
count_matrix.csv


title: AHRfl-13


title: F02754-TCR_Batch7

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

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

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.

value: CAR Product

tag: batch


title: SA_16

description:
104
count_matrix.csv


title: SA_15

description:
92
count_matrix.csv


title: F02736-GEX_F02755-FB_Batch7


title: F02620-TCR_Batch3


title: 18_1643_3

type: RNA

city: Gießen

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

hyb_protocol: 3.8 µg of fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S rat arrays for 16 h at 45°C and 60 rpm in an Applied Biosystems GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Applied Biosystems GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Applied Biosystems GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Bos taurus

source_name: Liver

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The study was conducted at the Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, Münchweiler an der Alsenz, Germany. All related procedures were approved by the Animal Welfare and Ethics Committee of the government of Coblenz, Rhineland Palatinate, Germany (permit no 23-177-07/G 19-20-008).   The design of the underlying study has been described in detail elsewhere (Wächter et al., 2022a). Briefly, 30 late-pregnant multiparous Holstein-Friesian dairy cows entering their second, third or fourth lactation were randomly assigned to one of the 2 experimental groups, that were fed a dry cow ration with either low (LP, 0.16% P in DM) or adequate P content (AP, 0.35% P in DM) during the last 4 wk of the dry period. The study cows were part of the herd of a research farm with an average 305-d milk yield of 12,500 kg. Dry cows and fresh cows were kept in separated areas of a freestall. Cows with signs of imminent parturition were moved to individual calving pens and if deemed to be clinically healthy proceeded to the lactation group within 24 of calving. From the moment of calving both groups were fed the same standard lactating cow ration with adequate P content. Lactating cows were milked twice daily between 04.30 h and 05.30 h and between 15.30 h and 16.30 h.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Karlsruhe) according to the manufacturer’s protocol. RNA quantity and quality were assessed spectrophotometrically using an Infinite 200M microplate reader equipped with a NanoQuant plate (both from Tecan, Mainz). The average RNA concentration and the A260/A280 ratio of all total RNA samples (n = 20, means ± SD) were 424 ± 78 ng/μL and 1.89 ± 0.05, respectively.

treatment_protocol: Study animals were fed a TMR formulated to meet or exceed requirements of dry or lactating cows, with exception of the P content of the LP dry cow ration (NRC, 2001). The dry cow base ration used in this experiment was based on corn silage, sugar beet pressed pulp silage, hay and straw. Pelleted concentrate, formulated for each treatment, was added to obtain the final TMR with the targeted P content (Supplementary Table S1). The dry cow diet of LP cows contained 0.16% P, while the P content of the TMR for AP cows was 0.35% P in DM. Mono-ammoniumphosphate (Windmill Monamphos FG, Aliphos Rotterdam BV, The Netherlands) was used as P supplement in the AP concentrate to obtain the targeted dietary P content in the AP ration. Urea was added to the LP concentrate to equalize the N content of both diets. The TMR was offered through electronic feeding gates (RIC System, Hokofarm Group, Marknesse, Netherlands) and was available ad libitum for lactating cows, but was restricted to 11.5 kg DM during the dry period for both treatments. Feed restriction in addition to a LP diet was necessary to maintain the daily P intake in LP cows below 20 g P/cow (Cohrs et al., 2018). Studies conducted on dry dairy cows indicated that counter regulation to P deprivation in the form of bone mobilization was consistently induced when dietary P supply did not exceed 20 g per cow and day, equivalent to approximately 80% of the currently recommended dietary P supply to dry cows during the last three weeks of gestation (Cohrs et al., 2022; NASEM, 2021). Water was available ad libitum.

value: Liver

tag: breed

value: Holstein-Friesian

value: postpartum

value: AP


title: 20_1711_3

value: LP


title: 16_1680_3


title: 14_1617_3


title: F02576-GEX_F02577-FB_Batch3


title: 10_1668_3


title: SA_14

description:
91
count_matrix.csv

value: Peripheral whole blood


title: patient C4P2, after first course of MP, B cells

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description:
Gene expression data for a patient with MS treated with methylprednisolone
C4P2-M1-T1-CD19

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.

source_name: B 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.

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

value: after

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

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: Rostock

tag: course of disease

value: SPMS

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

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: 12_1719_3

tag: tissue

tag: breed

tag: time

tag: group


title: patient C4P1, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C4P1-M1-T1-CD19

tag: patient id

tag: mp course

tag: time point

tag: cell population

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: male

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: yes

tag: study center

value: CIS/RRMS

value: new

value: hyperhidrosis


title: patient C4P1, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C4P1-M1-T0-CD19

tag: tissue

value: before

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

tag: number of other medications taken

tag: neurological dysfunction

tag: fs

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: patient C4P2, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C4P2-M1-T0-CD19

value: peripheral blood

tag: patient id

tag: mp course

tag: time point

tag: cell population

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)

value: bladder or bowel:yes


title: patient C3P1, after second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C3P1-M2-T1-CD4

source_name: T helper cells from the peripheral blood

tag: tissue

value: second

value: after

value: CD4+ T cells

value: non-responder

tag: body mass index

tag: current smoker

tag: study center

value: Jena

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: dimethyl fumarate

tag: number of other medications taken

tag: neurological dysfunction

value: recurring

tag: fs


title: SA_13

description:
81
count_matrix.csv

value: Peripheral whole blood

tag: disease category

value: Simple appendicitis (SA)


title: F02619-TCR_Batch3

value: CAR Product

tag: batch


title: SA_12

description:
79
count_matrix.csv


title: patient C2P8, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P8-M1-T1-CD19

tag: patient id

tag: mp course

value: first

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

value: female

tag: body weight (in kg)

value: Greifswald

value: CIS/RRMS

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: SA_11

description:
78
count_matrix.csv

tag: tissue

tag: disease category


title: patient C2P8, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P8-M1-T0-CD19

value: peripheral blood

tag: patient id

value: before

tag: body size (in cm)

tag: body mass index

tag: current smoker

tag: study center

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

tag: number of other medications taken

tag: neurological dysfunction

value: new

tag: fs

value: bladder or bowel:no


title: F02574-GEX_F02575-FB_Batch3

tag: batch


title: SA_10

description:
76
count_matrix.csv

tag: tissue


title: F03295-TCR_Batch15


title: F02323-GEX_F02325-FB_Batch1


title: SA_9

description:
73
count_matrix.csv

tag: disease category


title: F03285-GEX_F03286-FB_Batch15


title: SA_7

description:
65
count_matrix.csv


title: SA_8

description:
67
count_matrix.csv


title: 06_1675_3

value: Liver

tag: breed

value: Holstein-Friesian

tag: time

value: postpartum

tag: group

value: AP


title: F03298-TCR_Batch18


title: F03291-GEX_F03292-FB_Batch18


title: 02_1712_3

value: LP


title: patient C2P7, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P7-M1-T1-CD19

tag: patient id

tag: mp course

tag: time point

value: after

tag: cell population

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: male

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

tag: total dose of mp in mg

tag: days from first to last mp application

tag: side effects to mp


title: 08_1654_3

tag: tissue

tag: breed

tag: time

tag: group


title: 19_1711_2

value: antepartum


title: 04_1662_3


title: SA_6

description:
56
count_matrix.csv

value: Peripheral whole blood

tag: disease category

value: Simple appendicitis (SA)


title: 15_1680_2


title: F03976-TCR_Batch2

value: CAR Product

tag: batch


title: patient C2P7, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P7-M1-T0-CD19

tag: patient id

tag: mp course

value: first

tag: time point

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: study center

value: Greifswald

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

tag: number of other medications taken

tag: neurological dysfunction

tag: fs


title: patient C2P6, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P6-M1-T1-CD19

tag: tissue

value: peripheral blood

tag: patient id

tag: mp course

value: non-responder

tag: rna integrity number

tag: age (years)

tag: Sex

value: female

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: no

value: dimethyl fumarate

value: new

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: F02397-GEX_F02398-FB_Batch2

tag: batch


title: patient C3P1, before second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C3P1-M2-T0-CD4

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 (%)

value: yes

tag: study center

value: Jena

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

tag: number of other medications taken

value: recurring

value: bladder or bowel:no


title: patient C2P6, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P6-M1-T0-CD19

tag: tissue

tag: patient id

tag: mp course

value: first

value: CD19+ B cells

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

tag: neurological dysfunction

tag: fs

tag: total dose of mp in mg

tag: days from first to last mp application


title: 13_1617_2

value: Liver

tag: breed

value: Holstein-Friesian

tag: time

value: antepartum

tag: group

value: AP


title: patient C2P5, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P5-M1-T1-CD19

tag: tissue

value: peripheral blood

tag: time point

value: after

tag: cell population

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

value: female

tag: study center

value: Greifswald

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

tag: number of other medications taken

tag: side effects to mp


title: SA_4

description:
47
count_matrix.csv

value: Peripheral whole blood

tag: disease category

value: Simple appendicitis (SA)


title: patient C2P5, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P5-M1-T0-CD19

tag: tissue

tag: patient id

tag: mp course

value: before

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: yes

tag: neurological dysfunction

value: new

tag: fs

tag: total dose of mp in mg

tag: days from first to last mp application


title: F03258-TCR_Batch11

value: CAR Product

tag: batch


title: 09_1668_2

tag: breed

tag: time

tag: group


title: 17_1643_2

tag: tissue


title: SA_3

description:
40
count_matrix.csv

tag: disease category


title: SA_2

description:
25
count_matrix.csv


title: 11_1719_2


title: 07_1654_2

value: LP


title: SA_5

description:
49
count_matrix.csv


title: F03299-TCR_Batch19


title: F03293-GEX_F03294-FB_Batch19


title: F03254-GEX_F03256-FB_Batch11


title: patient C2P4, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P4-M1-T0-CD19

tag: patient id

tag: mp course

value: first

tag: time point

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

value: non-responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

value: male

value: no

tag: study center

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

tag: number of other medications taken

value: bladder or bowel:no

tag: side effects to mp


title: patient C2P4, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P4-M1-T1-CD19

tag: tissue

value: peripheral blood

tag: patient id

tag: mp course

value: after

tag: age (years)

tag: Sex

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

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


title: patient C2P3, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P3-M1-T1-CD4

tag: time point

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: study center

value: Greifswald

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

value: natalizumab


title: patient C2P3, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P3-M1-T0-CD4

tag: tissue

tag: patient id

tag: mp course

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: yes

tag: disease-modifying therapy

tag: number of other medications taken

tag: neurological dysfunction

value: new

tag: side effects to mp


title: SOX2KO_MO_rep1

city: Hangzhou

first: Bingjie

last: Hu

address: Yuhangtang Rd, Hangzhou, Zhejiang , China

institute: Zhejiang University

description:
SOX2KO
Cell metadata included in file on series record named "metadata.txt".

library_source: transcriptomic single cell

data_processing:
Reads were trimmed by Trimgalore to remove the bases with low quality and adapter sequences
The trimmed reads were align to ARS-UCD1.2  by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized  by Seurat
Assembly: ARS-UCD1.2
Supplementary files format and content: text files include normalized counts calculated by Seurat for each sample

source_name: embryo

extract_protocol:
Polyadenylated RNAs were captured and reverse transcribed with an Oligo(dT) primer
In brief, single cells were incubated at 72 °C for 3 min with lysis mixture. Reverse transcription and PCR pre-amplification were carried out with SuperScript II (Invitrogen) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems). After PCR amplification , the samples with different barcodes were mixed together and then purified with DNA Clean&Concentrator-5 (Zymo Research). The cDNAs of single cells were added with biotinylated index and purified using beads (Vazyme). The cDNAs were sheared into approximately 300 bp fragments using sonication (Covaries). The fragmented cDNAs were enriche by Dynabeads ® MyOne TM Streptavidin C1 (Invitrogen). Adaptor ligation and final library were conducted by NEBNext Library Quant Kit (New England Biolabs).

tag: developmental stage

value: Morula

tag: age

value: 6.0 day after fertilization

tag: treatment

value: embryos were injected with BE3 mRNA and SOX2 sgRNAs mix at zygote stage


title: SA_1

description:
8
count_matrix.csv

value: Peripheral whole blood

tag: disease category

value: Simple appendicitis (SA)


title: F03297-TCR_Batch17

tag: tissue

value: CAR Product

tag: batch


title: F02686-TCR_Batch5


title: Wild Type, Female, 3

city: Providence

first: Gregorio

last: Valdez

state: RI

address: 70 Ship Street

institute: Brown University

description: baseMean, Log2FoldChange, lfcSE, stat, pvalue, padj

data_processing:
Pre-trim QC using Fastqc and MultiQC
Adapter content trimming using Trimmomatic and TruSeq3-PE-2.fa
Post-trim QC using Fastqc and MultiQC
Alignment using Salmon
Differential gene expression using DESeq2 in R
Assembly: Mus musculus GRCm39

source_name: Soleus muscle

extract_protocol: RNA extraction from fresh frozen muscle; library preparation, Illumina, RNA with PolyA selection

value: Soleus muscle

tag: cell type

value: Muscle

tag: genotype

value: Wild type


title: SOX2NC_MO_rep1

description:
SOX2NC
Cell metadata included in file on series record named "metadata.txt".

value: embryos were injected with BE3 mRNA at zygote stage


title: Wild Type, Female, 4


title: patient C2P3, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P3-M1-T0-CD19

value: peripheral blood

tag: patient id

tag: mp course

value: first

tag: time point

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: female

tag: study center

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: fs

value: bladder or bowel:no

tag: total dose of mp in mg

tag: days from first to last mp application


title: embryo_rep6

description:
210811G
Cell metadata included in file on series record named "metadata.txt".

tag: developmental stage

value: multiplexed sample:Morula and blastocyst

tag: age

value: multiplexed sample:6.0,7.0,8.0,9.0 day after fertilization

tag: treatment

value: wildtype


title: Wild Type, Female, 1

tag: tissue

tag: cell type

tag: genotype


title: Wild Type, Female, 2


title: F02660-GEX_F02661-FB_Batch5

tag: batch


title: embryo_rep5

description:
210811E
Cell metadata included in file on series record named "metadata.txt".


title: F03289-GEX_F03290-FB_Batch17


title: 03_1662_2

value: Liver

tag: breed

value: Holstein-Friesian

tag: time

value: antepartum

tag: group

value: LP


title: 05_1675_2

value: AP


title: F03296-TCR_Batch16

value: CAR Product


title: Megf10 Knockout, Female, 4

value: Soleus muscle

value: Muscle


title: embryo_rep4

description:
210811D
Cell metadata included in file on series record named "metadata.txt".


title: 01_1712_2


title: Megf10 Knockout, Female, 3


title: F03287-GEX_F03288-FB_Batch16


title: embryo_rep3

description:
210811C
Cell metadata included in file on series record named "metadata.txt".


title: patient C2P3, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P3-M1-T1-CD19

value: peripheral blood

tag: patient id

tag: mp course

tag: time point

value: after

tag: cell population

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: yes

tag: study center

value: Greifswald

tag: course of disease

value: CIS/RRMS

tag: disease duration (years)

tag: disease-modifying therapy

value: natalizumab

tag: number of other medications taken

tag: neurological dysfunction

value: new

value: bladder or bowel:unchanged

tag: side effects to mp


title: patient C2P2, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P2-M1-T0-CD19

tag: tissue

tag: patient id

tag: mp course

value: first

tag: time point

value: before

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

value: responder

tag: percentage in pbmc

value: female

value: no

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

value: glatiramer acetate

tag: fs

value: bladder or bowel:no

tag: total dose of mp in mg

tag: days from first to last mp application


title: patient C2P1, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P1-M1-T1-CD4

value: CD4+ T cells

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

tag: study center

tag: course of disease

tag: disease duration (years)

tag: disease-modifying therapy


title: patient C2P2, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P2-M1-T1-CD19

tag: tissue

value: peripheral blood

tag: patient id

tag: mp course

tag: time point

tag: cell population

tag: clinical evaluation

tag: percentage in pbmc

tag: number of relapses in the past 2 years

tag: duration since last relapse (months)

tag: edss score

tag: number of other medications taken

tag: neurological dysfunction

tag: side effects to mp


title: patient C2P1, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P1-M1-T1-CD19

value: after

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

tag: study center

tag: fs

tag: total dose of mp in mg

tag: days from first to last mp application


title: Megf10 Knockout, Female, 2

tag: tissue

value: Soleus muscle

tag: cell type

value: Muscle

tag: genotype


title: F03267-TCR_Batch13

value: CAR Product

tag: batch


title: Megf10 Knockout, Female, 1


title: embryo_rep2

description:
210811B
Cell metadata included in file on series record named "metadata.txt".

tag: developmental stage

value: multiplexed sample:Morula and blastocyst

tag: age

value: multiplexed sample:6.0,7.0,8.0,9.0 day after fertilization

tag: treatment

value: wildtype


title: embryo_rep1

description:
210811A
Cell metadata included in file on series record named "metadata.txt".


title: F03263-GEX_F03265-FB_Batch13


title: shRad21_2_3 [R3_3]

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

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 shRad21 #2

tag: time


title: patient C2P1, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P1-M1-T0-CD19

tag: patient id

tag: mp course

value: first

tag: time point

value: before

tag: cell population

value: CD19+ B cells

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: Sex

value: yes

value: Greifswald

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

tag: number of other medications taken

tag: neurological dysfunction

value: new

tag: side effects to mp


title: F03248-TCR_Batch10

tag: tissue

tag: batch


title: Lineage tracing rep1, ube2e1 scars

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: Targeted library for CRISPR lineage tracing

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.

value: adult brain

tag: cell type

value: mixed (tissue dissociation)

tag: genotype


title: shRad21_2_1 [R3_1]

tag: treatment

tag: time


title: F03246-GEX_F03247-FB_Batch10

value: CAR Product


title: patient C2P1, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C2P1-M1-T0-CD4

value: peripheral blood

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: 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

tag: study center

tag: fs

value: bladder or bowel:no

tag: total dose of mp in mg

tag: days from first to last mp application


title: Lineage tracing rep1, rpl39 scars

tag: tissue

tag: cell type

tag: genotype


title: shRad21_2_2 [R3_2]

value: Primary mouse neural stem cells

value: wild type (Phf2flox/flox)

tag: treatment

tag: time


title: patient C1P5, after second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P5-M2-T1-CD4

tag: patient id

tag: mp course

value: second

tag: time point

value: after

tag: cell population

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: Sex

value: male

value: Berlin

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: ocrelizumab

tag: number of other medications taken

tag: neurological dysfunction

value: bladder or bowel:unchanged

tag: side effects to mp

value: cardiovascular problems


title: F03306-TCR_Batch9

tag: tissue

tag: batch


title: Lineage tracing rep1, cirbpb scars

tag: cell type

tag: genotype


title: patient C1P5, before second course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P5-M2-T0-CD4

tag: patient id

tag: mp course

tag: time point

value: before

tag: cell population

tag: clinical evaluation

value: responder

tag: purity (%)

tag: rna integrity number

tag: age (years)

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

value: yes

tag: study center

value: CIS/RRMS

value: new

tag: fs

tag: total dose of mp in mg

tag: days from first to last mp application


title: shRad21_1_3 [R2_3]

tag: cell type

tag: genotype

tag: treatment

value: wild type (Phf2flox/flox) control, infect shRad21 #1

tag: time


title: F02985-GEX_F02986-FB_Batch9

tag: tissue

value: CAR Product

tag: batch


title: Lineage tracing rep1, cfl1 scars

value: adult brain

value: mixed (tissue dissociation)


title: shRad21_1_2 [R2_2]

value: Primary mouse neural stem cells

value: wild type (Phf2flox/flox)


title: F03268-TCR_Batch14


title: Lineage tracing rep1, actb2 scars


title: shRad21_1_1 [R2_1]


title: shNT_3

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


title: Lineage tracing rep1, actb1 scars


title: patient C1P5, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P5-M1-T0-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

value: non-responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: Sex

value: male

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

tag: number of other medications taken

tag: neurological dysfunction

value: bladder or bowel:no

tag: side effects to mp


title: F03305-TCR_Batch8

tag: tissue

tag: batch


title: patient C1P5, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P5-M1-T1-CD4

tag: patient id

tag: mp course

tag: time point

value: after

tag: cell population

tag: rna integrity number

tag: age (years)

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

tag: study center

value: Berlin

value: ocrelizumab

tag: fs

value: bladder or bowel:unchanged

tag: total dose of mp in mg

tag: days from first to last mp application


title: Brain 20 - sorted, scRNAseq

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

tag: tissue region

value: sorted

tag: cell type

tag: genotype


title: patient C1P4, after first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P4-M1-T1-CD4

tag: tissue

tag: patient id

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

tag: Sex

value: female

value: no

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: glatiramer acetate

tag: number of other medications taken

tag: neurological dysfunction

value: recurring

tag: side effects to mp


title: patient C1P4, before first course of MP, T cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P4-M1-T0-CD4

value: peripheral blood

tag: mp course

tag: time point

value: before

tag: cell population

tag: rna integrity number

tag: age (years)

tag: body weight (in kg)

tag: body size (in cm)

tag: body mass index

tag: current smoker

tag: study center

tag: fs

tag: total dose of mp in mg

tag: days from first to last mp application


title: patient C1P4, after first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P4-M1-T1-CD19

tag: tissue

tag: patient id

value: first

value: CD19+ B cells

tag: clinical evaluation

tag: percentage in pbmc

tag: cells per ml

tag: purity (%)

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


title: Brain 19 - whole, scRNAseq

value: adult brain

tag: tissue region

value: whole

tag: cell type

value: mixed (tissue dissociation)

tag: genotype


title: shNT_2

value: Primary mouse neural stem cells

value: wild type (Phf2flox/flox)

tag: treatment

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

tag: time


title: F02981-GEX_F02982-FB_Batch8

tag: tissue

value: CAR Product

tag: batch


title: F03257-TCR_Batch12


title: Brain 18 - rhombencephalon, scRNAseq

value: rhombencephalon

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


title: Input-2

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

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

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

value: embryonic stem cells


title: patient C1P4, before first course of MP, B cells

description:
Gene expression data for a patient with MS treated with methylprednisolone
C1P4-M1-T0-CD19

tag: patient id

tag: mp course

tag: time point

tag: cell population

tag: clinical evaluation

value: responder

tag: percentage in pbmc

tag: cells per ml

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

value: CIS/RRMS

tag: number of other medications taken

tag: neurological dysfunction

tag: fs

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: Brain 18 - mesencephalon, scRNAseq

tag: tissue

tag: tissue region

value: mesencephalon

tag: cell type

tag: genotype


title: F03253-GEX_F03255-FB_Batch12

tag: batch