title: Cygb WT left ventricle, 2 weeks Ang II, 3

city: Albany

first: David

last: Jourd'heuil

address: 43 New Scotland Ave

department: Molecular and Cellular Physiology

institute: Albany Medical College

description:
Library name: Sample WT_Ang II_3
column name in counts_all_samples.txt: WT_Ang II_3

data_processing:
Differential gene expression analysis was conducted using DESeq2 in R.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts for each Sample

source_name: heart, left ventricle

growth_protocol: All experiments involving mice were approved by the Institutional Animal Care and Use Committee at Albany Medical College. Adult global wildtype and cytoglobin knockout mice were generated as previously described.

extract_protocol:
At the end of the two-week infusion period, total RNA was extracted from from left ventricular tissue using Trizol Reagent according to the manufacture’s protocol.
The RNA samples were sent to GENEWIZ (Azenta Life Sciences) for RNA library, preparation, sequencing.

treatment_protocol: The mice were anesthetized using isoflurane (with 1–2% oxygen) before a subcutaneous pocket was created through a 1 cm mid-scapular incision. A 14-day osmotic pump (Alzet Model 1002) loaded with angiotensin-II at a dosage of 1.5 mg/kg/day was inserted into the pocket. The incision was closed with sutures.

value: heart, left ventricle

tag: genotype

tag: treatment

value: Angiotensin II


title: hlsec, Vehicle, Hi-C, rep1

status: Public on Mar 10 2026

type: SRA

city: Chengdu

first: Enjiang

last: Lai

address: 37 Guoxue Alley

country: China

institute: Sichuan University

description: Library name: Vehicle_R1

library_source: genomic

data_processing:
Hi-C reads were processed using the Hi-C Pro pipeline (v3.1.0). Reads were first aligned to the hg38 reference genome using bowtie2, the aligned reads were assigned to MboI restriction fragments, and the interaction pairs were reconstructed. Then quality assessment was performed, singletons and multi-hit pairs and failed ligation products were filtered. The remaining valid pairs were then used to build contact matrices, and then normalized by iterative correction and eigenvector decomposition.
Assembly: hg38
Supplementary files format and content: hic files of Hi-C juicebox contact map

molecule: genomic DNA

organism: Homo sapiens

source_name: Human liver sinusoidal endothelial cells

extract_protocol:
Hi-C library preparation was carried out following existing protocols. Briefly, approximately 100,000 to 1,000,000 cell pellets were used as input per sample. Nuclei were digested overnight with MboI at 37 °C, followed by end-labeling of the DNA with biotin using 25 μl of fill-in master mix at 37 °C for 2 hours. The DNA was then ligated using 450 μl of ligation master mix at room temperature for 4 hours. DNA was purified using phenol-chloroform extraction. To remove linear DNA, the sample was treated with Lambda exonuclease (NEB) and of Exonuclease I (NEB) at 37 °C for 30 minutes. Fragmentation of 100–500 ng of DNA was performed using the TruePrep DNA Library Prep Kit V2 (Vazyme).
Biotin-labeled DNA was enriched by pull-down with Dynabeads MyOne Streptavidin T1 beads (Life Technologies). Library amplification and size selection were conducted using TruePrep Amplify Enzyme (Vazyme) and SPRIselect Beads (Beckman Coulter). Libraries were sequenced on Illumina platform.

treatment_protocol: Low-passage cells were starved with basal endothelial medium for 2 hours followed by treatment with BRD4 inhibitor (iBET151, 2.5 umol/L, Selleck, S2780) for 2 hours. Then, human recombinant TNFα (50 ng/mL; PeproTech, 300-01A) was treated to hLSECs for 6 hours before cells were collected for further analysis.

tag: cell type

value: DMSO


title: Cygb WT left ventricle, 2 weeks Ang II, 2

state: NY

country: USA

description:
Library name: Sample WT_Ang II_2
column name in counts_all_samples.txt: WT_Ang II_2

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue


title: TBM, blood,  GSH009, D7

city: London

first: James

middle: Royce

last: Barnacle

state: London

address: Francis Crick Institute, 1 Midland Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description: Library name: DAV1202A128

data_processing:
Raw data were processed using nf-core/rnaseq (v3.10.1) of the nf-core collection of workflows. This workflow used FASTQ files as input, performed quality control (QC), trimming and (pseudo-)alignment to the GRCh38 release 95 human reference genome, and produced a gene expression matrix and QC report. The pipeline was executed with Nextflow (v22.10.3). The output matrix was read into R (v4.2.0) in which subsequent analysis was done.
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: .csv file with samples as colnames and genes as rownames

molecule: total RNA

source_name: Blood

extract_protocol:
Whole blood was collected directly into PAXgene RNA tubes (QIAGEN/BD Biosciences) from 40 patients enrolled into the LASER-TBM trial. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN, Venlo, Netherlands). Samples were stored at -80˚C before and after RNA extraction. Quantity and quality of RNA was assessed using a Qubit fluorimeter (ThermoFisher) and Agilent 2100 Bioanalyzer. Samples with RNA integrity number (RIN) <7 were excluded.
RNA libraries were constructed using Tecan’s Universal Human Blood RNA-Seq kit. Ribosomal and globin RNA were removed using Tecan’s AnyDeplete system. DNA library size distribution was assessed using the D1000 TapeStation kit processed on the 4200 TapeStation (Agilent Technologies). The data were analysed by Agilent’s 4200 TapeStation Analysis Software. Concentration was measured using the QuantiFluor dsDNA System (Promega Corporation). Libraries were sequenced on an Illumina HiSeq4000 with a single-end 100 cycle read configuration.

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: female

tag: antibiotics

value: intensified

tag: aspirin

value: no

tag: diagnosis

value: probable

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: hlsec, iBET151, ATAC, rep1

description: Library name: iBET151_ATAC_R1

data_processing:
ATAC-seq data was first quality assessed using the ChIPQC package (v1.21.0). The reads were then mapped to the human reference genome hg38 using bowtie2 (v2.3.1). Duplicated mapped reads were discarded using the MarkDuplicates function from Picard (v2.25.6). Narrow peaks were identified utilizing MACS2.
Assembly: hg38
Supplementary files format and content: BigWig files of genome wide ATAC-seq results

extract_protocol:
Cells were washed with cold PBS, and then centrifuged for 5 minutes. Then the cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630), followed by centrifugation for 10min at 4 °C. The pellets were resuspended in transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina), and 22.5 μL nuclease-free water), and transposition was carried out for 30 minutes at 37 °C.
The sample was then purified and DNA was amplified with PCR. The libraries were then sequenced on the Illumina platform.

value: Human liver sinusoidal endothelial cells


title: TBM, blood,  NSH010, D56

description: Library name: DAV1202A126

value: soc

value: definite

value: positive


title: hlsec, Tnfa, ATAC, rep2

description: Library name: Tnfa_ATAC_R2

value: Tnfa


title: RNA-seq of single blastomere (2cell_E05_B2)

city: Fuchu

first: Satoshi

last: Sugimura

state: Tokyo

address: 3-5-8 Saiwai-cho

country: Japan

institute: Tokyo Uiniversity of Agriculture and Technology

description: Library name: 2cell_E05_B2

data_processing:
Adapter trimming was performed using Trim Galore.
Sequence quality was assessed with FastQC.
Reads were aligned to the bovine reference genome (ARS-UCD1.2/bosTau9) using STAR.
Transcript quantification was performed using RSEM.
Assembly: ARS-UCD1.2/bosTau9
Supplementary files format and content: Gene-level count matrix generated by RSEM, provided as tab-delimited text files. Each file contains Ensembl gene IDs and corresponding TPM and expected count values for each sample.

organism: Bos taurus

source_name: blastomerer derived from IVF

growth_protocol: Bovine embryos were produced by in vitro fertilization (IVF) using cumulus-oocyte complexes (COCs) collected from slaughterhouse-derived ovaries. COCs were matured and fertilized in vitro, and then cultured in a time-lapse incubator at 38.5°C under 5% CO₂, 5% O₂, and 90% N₂ until the desired developmental stage.

extract_protocol:
Total RNA was extracted from single blastomeres using the SMART-Seq HT PLUS Kit (Takara Bio, Shiga, Japan), with modifications for single-cell analysis.
Reverse transcription and cDNA amplification were performed using the SMART-Seq HT PLUS Kit (Takara Bio, Shiga, Japan). cDNA quality was evaluated using an Agilent 2200 TapeStation with High Sensitivity D5000 ScreenTape (Agilent Technologies). Libraries were sequenced on the NovaSeq 6000 platform (Illumina) with 150 bp paired-end reads.

treatment_protocol: Not applicable. No experimental treatment was performed.

value: blastomerer derived from IVF

tag: Stage

tag: embryo id

tag: blastomere id


title: Cygb WT left ventricle, 2 weeks Ang II, 1

description:
Library name: Sample WT_Ang II_1
column name in counts_all_samples.txt: WT_Ang II_1

tag: tissue

tag: genotype

tag: treatment


title: hlsec, iBET151, ATAC, rep2

description: Library name: iBET151_ATAC_R2

tag: cell type


title: hlsec, Vehicle, Hi-C, rep2

description: Library name: Vehicle_R2


title: spleen CD8+ T cells, KLF2 KO, D25, Rep 1

city: Minneapolis

first: Christine

middle: H

last: O'Connor

address: 117 Pleasant St. SE

department: Minnesota Supercomputer Institute

institute: University of Minnesota

description: Library name: D25_KLF2_KO_1

data_processing:
Reads were trimmed using trimmomatic
Samples were aligned using HISAT2 v2.1.0
featureCounts v2.0.6 (Liao et al., 2014) was used to count mapped reads to genes
DE analysis was performed using EdgeR in R
Assembly: GRCm39.109
Supplementary files format and content: raw_counts.txt: raw gene counts for all samples
Supplementary files format and content: D25_Klf2_fullanno.txt: noramlized counts, DE results and gene annotation information for D25 KLF2 KO and matched controls
Supplementary files format and content: D25_Klf3_fullanno.txt: noramlized counts, DE results and gene annotation information for D25 KLF3 KO and matched controls
Supplementary files format and content: D7_Klf2_fullanno.txt: noramlized counts, DE results and gene annotation information for D7 KLF2 KO and matched controls

source_name: spleen

extract_protocol:
RNA was extracted using Qiagen Rneasy Plus Micro Kit. >500ng RNA was used to generate sequencing library.
RNA libraries for RNA-sequencing were prepared using TakaraBio PicoMammalian V2 kit following manufacturer's protocol. TakaraBio PicoMammalian V2 Library preparation

treatment_protocol: Congenically distinct WT or KLF2-GFP P14 CD8+ T cells were negatively enriched from spleen and activated with plate bound α-CD3 and α-CD28 with rhIL-2 for 48 hours, and then electroporated with sgRNAs/Cas9 complexes for target (Klf2 or Klf3) or control (Cd19 or Thy1) genes through a Lonza 4DNucleofector X Unit, using published conditions (Seki et al. 2018). Following culture in rhIL-2 for 24-48h, 5x10e4 CRISPR-modified cells were co-adoptively transferred into congenically distinct host mice, which received LCMV-Arm infection (2x10e5 PFU) within 2h of transfer. CRISPR modified donor P14 CD8+ T cells were FACS sorted from the spleen, 8- or 25-days post LCMV infection.

value: spleen


title: hlsec, Tnfa, ATAC, rep1

description: Library name: Tnfa_ATAC_R1


title: TBM, blood,  MPH016, D7

description: Library name: DAV1202A124

tag: patient id

tag: study

tag: timepoint

tag: age


title: RNA-seq of single blastomere (2cell_E05_B1)

description: Library name: 2cell_E05_B1


title: Cygb KO left ventricle, 2 weeks Ang II, 3

description:
Library name: Sample KO_Ang II_3
column name in counts_all_samples.txt: KO_Ang II_3

value: heart, left ventricle


title: TBM, blood,  MPH044, D0

description: Library name: DAV1202A125

tag: Sex

value: male

tag: antibiotics

tag: aspirin

tag: diagnosis


title: RNA-seq of single blastomere (2cell_E04_B2)

description: Library name: 2cell_E04_B2


title: TBM, blood,  MPH036, D56

description: Library name: DAV1202A122

value: yes

tag: gxpu

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Cygb KO left ventricle, 2 weeks Ang II, 1

description:
Library name: Sample KO_Ang II_1
column name in counts_all_samples.txt: KO_Ang II_1

value: Angiotensin II


title: Cygb KO left ventricle, 2 weeks Ang II, 2

description:
Library name: Sample KO_Ang II_2
column name in counts_all_samples.txt: KO_Ang II_2


title: hlsec, Vehicle, ATAC, rep1

description: Library name: Vehicle_ATAC_R1

value: DMSO


title: RNA-seq of single blastomere (2cell_E03_B2)

description: Library name: 2cell_E03_B2

tag: Stage

tag: embryo id

tag: blastomere id


title: Uterus Transplant 5_Biopsy 3_L2_GEX

city: Birmingham

first: Rebecca

last: Asiimwe

state: Alabama

address: 1720 2nd Ave South

department: Surgery

institute: The University of Alabama at Birmingham

description:
Library name: UTx05Bx03-1_S32_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

data_processing:
Reads from single-cell RNA-seq experiments of each Healthy Control and Uterus Transplant library were pre-processed and aligned against the GRCh38 human reference and quantified using Cell Ranger (v.6.1.1) from 10x Genomics
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-separated values files (tsv) and matrix files (mtx): *_barcodes.tsv.gz: cellular barcodes present in dataset; *_features.tsv.gz: IDs of quantified genes; *_matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs and columns correspond to the cellular barcodes
Library strategy: CITE-seq

source_name: Endometrium

extract_protocol:
Endometrial biopsies were collected with a Pipelle® suction curette (Cooper Surgical; Ref. 8200) in the clinical setting and transported to the laboratory in DPBS with calcium and magnesium (DPBS+/+; Gibco™; Cat. 14-040-133) on ice. Multiple passes of the suction curette were performed to acquire sufficient tissue for multimodal analysis. Endometrial biopsies were then digested to isolate cells for downstream analysis including sorting, flow cytometry, or in vitro incubation. Endometrial biopsies used for immunofluorescence microscopy were embedded in O.C.T. mounting media (Tissue-Tek; Cat. No. 4583) in a mold (Tissue-Tek; Cat. No. 4566). Molds were then placed in liquid nitrogen-cooled isopentane (Fisher Scientific; Cat. No. O3551-714 4). Frozen molds were stored at -800C until sectioned onto glass slides for imaging. Endometrial biopsies used for single cell isolation were processed into single cell suspensions for use in downstream single cell isolation techniques, such as scRNA-seq, spectral flow cytometric analysis, and in vitro culture. The biopsies were minced in a petri dish containing 2-3 mL of 370C-warmed DPBS with Calcium and Magnesium (DPBS+/+) on ice with a razor blade or scalpel and transferred to a 50 mL conical for digestion, also on ice. The petri dish was rinsed 4-5 times with 1 mL of 370C-warmed DPBS+/+ which was also transferred to the 50 mL conical. A 1:100 ratio of 5mg/mL Liberase (Sigma Aldrich; 723 SKU 5401127001) and a 1:1000 ratio of 1 mg/mL DNAse I (Sigma-Aldrich; SKU 724 11284932001) was added to the conical and inverted 2-3 times to mix. The conical 725 containing the minced biopsy and digestion media was then placed in a 370C shaking incubator at 240 RPMs and was inspected every 5 minutes to determine if the digestion had completed. If the digestion needed to continue, the conical was inverted 2-3 times to mix and placed back in the 370C shaking incubator at 240 RPMs. Digestion typically took 10-15 minutes on average. The digested sample was placed on ice and filtered through a 70 μm strainer (Stemcell Technologies; Cat. 27260) into a new 50 mL conical. The strainer was rinsed 5 times with 1 mL ice-cold DPBS+/+ before adding more ice-cold DPBS+/+ to the 50mL mark. The digested biopsy was then centrifuged at 300xg for 5 min at 4ºC. After centrifugation, the supernatant was aspirated without disturbing the pellet, which was then transferred to a 15mL conical and resuspended in 2 mL ACK lysis buffer (Quality Biological; Cat. 118-156-101) to incubate on ice for 2 minutes. After ACK lysis, 13 mL ice-cold DPBS without calcium and magnesium (DPBS-/-; Gibco™; Cat. 14-287-739 080) was added to the cell suspension. The 15 mL conical was then inverted 2-3 times to mix and was then centrifuged at 300xg for 5 min at 4ºC. The supernatant was aspirated without disturbing the cell pellet which was then resuspended in 0.5-1mL fresh sort buffer (ice-cold DPBS-/- + 0.04% (w/v) BSA (Jackson ImmunoResearch; Cat. 001-000-162)) for counting. Cells were counted by creating a 1:10 or 1:100 dilution with 0.04% Trypan blue in PBS (Gibco™; Ref. 15250-061). For the 1:10 dilution, 10 μL of the well-mixed cell suspension was added to 90 μL of 0.04% Trypan blue in PBS. For a 1:100 dilution, 10 μL of the 1:10 dilution was added to 90 μL of 0.04% Trypan blue in PBS. Cell counts were performed using a disposable Neubauer improved hemocytometer (INCYTO; DHC-N01-748 5), following the manufacturer’s instructions.
Live CD45+ cells were used for single-cell RNA sequencing after being FACS-enriched. Cells that were used in CITE-seq experiments were blocked with TruStain Fc block (BioLegend; Cat. 422301) for 30 minutes. Cells were then incubated with TotalSeq B™ Universal cocktail (BioLegend; Cat. 399904) in Cell Staining Buffer (Biolegend; Cat. 420201) and washed following the manufacturer’s protocol before being used for scRNA library preparation. Cells isolated for scRNA/CITE-seq were suspended in ice-cold cell sorting buffer. scRNA GEMs and libraries were prepared according to the manufacturer's instructions. 5' libraries were prepared according to 10x Genomics CG000331 protocol, using Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics; PN-1000263). 3' libraries were prepared using 10x Genomics CG000399 protocol, or CG000206 if a CITE-seq antibody panel was used with the appropriate 3’ GEM kit (10x Genomics; PN 1000121). Both 3' and 5' libraries used Dual Index Kit TT Set A (10x Genomics; PN 3000431). GEMs were created on either a Chromium Controller or Chromium X (10x Genomics). Either C1000 (Bio-rad) or SimpliAmp (Applied Biosystems) thermocyclers were used for library prep. Quality and concentrations of cDNA and final libraries were calculated from 2100 BioAnalyzer (Agilent) electrograms. Sequencing was performed on a NovaSeq 6000 (Ilumina)

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

tag: tissue

value: Endometrium

value: CD45+ Cells

tag: genotype

value: XX

tag: treatment

value: Uterus Transplant


title: CnT_n_aIgG_rep2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Library name: CnT_n_aIgG_rep2

data_processing:
FASTQ files were processed using nf-core/cutandrun pipeline v3.2.2. In this pipeline, Bowtie2 was used for alignment to mm10, and peaks were called with SEACR and MACS2 using IgG controls as reference.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Spleen

extract_protocol:
P14 T  cells were sorted from naïve or day 8 post-infection spleens.
Libraries were prepared following the Bench Top CUT&Tag v3 protocol by Steven Henikoff lab (Hatice S Kaya-Okur, 2020; Kaya-Okur et al., 2019) with minor modifications. Briefly, 200,000 live cells were lysed, nuclei isolated and bound to concanavalin A beads (EpiCypher). Nuclei were incubated overnight with anti-KLF2 antibody (MilliporeSigma  #09820) or Rabbit IgG (EpiCypher #13-0042). Anti-Rabbit Secondary Antibody (EpiCypher #13-0047) and pAG-Tn5 (EpiCypher) were added the next day. Tagmentation was performed in 50 μL of Tagmentation Buffer for 1 hour at 37°C in a thermocycler. The reaction was stopped by adding 3 μL of 0.5 M EDTA, 1 μL of 10% SDS, and 1 μL of Proteinase K (25 mg/10 mL in H2O), followed by incubation at 50°C for 1 hour. DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) and purified with the MinElute Reaction Cleanup Kit (Qiagen). Libraries were amplified with dual indexed adaptors.

value: Spleen

tag: cell type

value: P14 Cells

value: WT

value: control

tag: chip antibody

value: IgG


title: hlsec, Vehicle, ATAC, rep2

description: Library name: Vehicle_ATAC_R2

value: Human liver sinusoidal endothelial cells


title: RNA-seq of single blastomere (2cell_E04_B1)

description: Library name: 2cell_E04_B1

value: blastomerer derived from IVF


title: RNA-seq of single blastomere (2cell_E03_B1)

description: Library name: 2cell_E03_B1


title: Uterus Transplant 5_Biopsy 3_L1_ADT

description:
Library name: UTx05Bx03-1FB_S33_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

library_source: other

molecule: protein

value: ADT


title: TBM, blood,  MPH041, D0

description: Library name: DAV1202A120

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: male

tag: antibiotics

value: intensified

value: no

value: possible

value: negative

tag: blood neutrophils


title: CnT_n_aKLF2_rep2

description: Library name: CnT_n_aKLF2_rep2


title: CnT_n_aIgG_rep1

description: Library name: CnT_n_aIgG_rep1


title: RNA-seq of single blastomere (2cell_E02_B2)

description: Library name: 2cell_E02_B2

tag: Stage


title: TBM, blood,  MPH033, D56

description: Library name: DAV1202A118

value: female

value: soc

tag: aspirin

tag: diagnosis

value: definite

tag: gxpu

value: positive

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Uterus Transplant 3_Biopsy 3_L1_4_GEX

description:
Library name: UTx03Bx03-2_S35_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

tag: tissue

value: Endometrium

value: CD45+ Cells

tag: genotype

value: XX

tag: treatment

value: Uterus Transplant


title: RNA-seq of single blastomere (2cell_E02_B1)

description: Library name: 2cell_E02_B1

tag: cell type

value: blastomerer derived from IVF

tag: embryo id

tag: blastomere id


title: TBM, blood,  GSH011, D0

description: Library name: DAV1202A121

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

tag: antibiotics

value: probable


title: TBM, blood,  MPH038, D7

description: Library name: DAV1202A119

value: male

value: intensified

tag: aspirin

value: no

tag: diagnosis

tag: gxpu

tag: mtb culture

tag: blood neutrophils


title: TBM, blood,  MPH018, D14

description: Library name: DAV1202A117

tag: tissue

value: negative

tag: hiv vl

tag: blood wcc


title: Uterus Transplant 3_Biopsy 3_L1_2_GEX

description:
Library name: UTx03Bx03-1_S34_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

tag: adt

tag: cell type

tag: genotype

tag: treatment


title: CnT_D8_aIgG_rep2

description: Library name: CnT_D8_aIgG_rep2

value: Spleen

value: P14 Cells

value: WT

value: LCMV Armstrong

tag: chip antibody

value: IgG


title: RNA-seq of single blastomere (2cell_E01_B2)

description: Library name: 2cell_E01_B2

tag: Stage

tag: embryo id

tag: blastomere id


title: Uterus Transplant 3_Biopsy 3_L1_3_ADT

description:
Library name: UTx03Bx03-2FB_S37_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: ADT

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium


title: CnT_D8_aIgG_rep1

description: Library name: CnT_D8_aIgG_rep1


title: CnT_n_aKLF2_rep1

description: Library name: CnT_n_aKLF2_rep1

value: control


title: TBM, blood,  GSH005, D56

description: Library name: DAV1202A116

tag: patient id

tag: study

tag: timepoint

tag: age

tag: Sex

tag: antibiotics

tag: aspirin


title: RNA-seq of single blastomere (2cell_E01_B1)

description: Library name: 2cell_E01_B1

value: blastomerer derived from IVF


title: Uterus Transplant 3_Biopsy 3_L1_1_ADT

description:
Library name: UTx03Bx03-1FB_S36_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: tissue

value: CD45+ Cells

value: XX

value: Uterus Transplant


title: TBM, blood,  NSH004, D0

description: Library name: DAV1202A115

value: Blood

value: laser

value: female

value: soc

tag: diagnosis

value: possible

tag: gxpu

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: CnT_D8_aKLF2_rep4

description: Library name: CnT_D8_aKLF2_rep4

value: Spleen

tag: cell type

value: P14 Cells

tag: genotype

tag: treatment

tag: chip antibody


title: TBM, blood,  GSH002, D56

description: Library name: DAV1202A114

tag: patient id

tag: study

value: male

value: no

value: negative


title: Uterus Transplant 3_Biopsy 2_L4_ADT

description:
Library name: UTx03Bx02FB_S57_L004
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: ADT

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1


title: TBM, blood,  MPH036, D7

description: Library name: DAV1202A112

tag: timepoint

tag: age

tag: Sex

tag: antibiotics

value: intensified

value: yes

value: definite

value: positive


title: CnT_D8_aKLF2_rep3

description: Library name: CnT_D8_aKLF2_rep3

tag: tissue

value: WT

value: LCMV Armstrong


title: TBM, blood,  NSH011, D0

description: Library name: DAV1202A113

value: Blood

value: laser

tag: aspirin

tag: diagnosis

tag: gxpu

tag: mtb culture


title: RNA-seq of single blastomere (1cell_E08_B1)

description: Library name: 1cell_E08_B1

tag: cell type

value: blastomerer derived from IVF

tag: Stage

tag: embryo id

tag: blastomere id


title: Uterus Transplant 3_Biopsy 2_L1_ADT

description:
Library name: UTx03Bx02FB_S57_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: Endometrium

value: CD45+ Cells

tag: genotype

value: XX

tag: treatment

value: Uterus Transplant


title: CnT_D8_aKLF2_rep2

description: Library name: CnT_D8_aKLF2_rep2

value: Spleen

value: P14 Cells

tag: chip antibody


title: RNA-seq of single blastomere (1cell_E07_B1)

description: Library name: 1cell_E07_B1


title: CnT_D8_aKLF2_rep1

description: Library name: CnT_D8_aKLF2_rep1


title: TBM, blood,  NSH015, D56

description: Library name: DAV1202A111

tag: patient id

tag: study

value: male

value: no

value: possible

value: negative

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: RNA-seq of single blastomere (1cell_E10_B1)

description: Library name: 1cell_E10_B1


title: Uterus Transplant 3_Biopsy 2_L3_ADT

description:
Library name: UTx03Bx02FB_S57_L003
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: ADT

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

tag: tissue


title: TBM, blood,  GSH009, D56

description: Library name: DAV1202A110

tag: timepoint

tag: age

tag: Sex

value: female

tag: antibiotics

value: intensified

tag: aspirin

tag: diagnosis

value: probable

tag: gxpu


title: RNA-seq of single blastomere (1cell_E06_B1)

description: Library name: 1cell_E06_B1

tag: cell type

tag: Stage

tag: embryo id

tag: blastomere id


title: Day 5 Lrig1 M5B 2

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

institute: Vanderbilt University Medical Center

description:
Library name: 12076_4
PIP-seq T-20 V.4

library_source: transcriptomic single cell

data_processing:
Libraries were processed utilizing the DropEst pipeline, as previously described 43. Sequences were aligned with PIPSeeker version v3.30, adding the eYFP sequence (GenBank: KM486813.1) to the reference genome GRCm39 release M29. The high-quality cells were identified using a combination of the dropkick algorithm. Normalization, inverse hyperbolic sine transformation, and Z-score scaling were performed on cells as an AnnData object utilizing the Scanpy toolkit. The matrices were projected into two dimensions using a UMAP initialization based on their 50 principal component decomposition. Final selection of cell-containing droplets was made based on multiple quality metrics including mitochondrial count percentages, total reads, and gene-expression profiles.
Assembly: GRCm39 release M29
Supplementary files format and content: Tab-separated values and matrix files

source_name: Small intestine

extract_protocol:
The first 5 cm of jejunum were isolated, linearized, and washed with PBS. Muscle was removed by mechanical dissection. Epithelial cells were separated from the underlying lamina propria by incubating in chelation buffer (3 mM EDTA and 20 mM HEPES) for 1hr at 4°C and vigorously shaking in PBS. Epithelial and lamina propria cells were then processed separately, simultaneously. Epithelial cells were dissociated into a single cell suspension by incubating in cold protease buffer (100 mg/mL Protease and 5 mg/mL DNase) on a rotator for 25 minutes at 4°C, gentle pipetting with a P1000, and passing through a 70 µm filter. The lamina propria was placed in chelation buffer, rotated at 37°C for 20 minutes, and vigorously shaken to remove in remaining epithelial cells. Stromal cells were dissociated into a single cell suspension by mincing, incubating in lamina propria dissociation buffer (25 mg/mL Liberase and 5 mg/mL DNase) on a rotator for 30 minutes at 37°C, gently mixing using a 1-mL-syringe, and passing through a 70 µm filter. Cells were quenched with 2% FBS and underwent a series of washes with 0.02% BSA in PBS. Epithelial and lamina propria cells were combined 50/50 at a concentration of 5000 viable cells/µL in PIPseq sample buffer.
Library was prepared for scRNA-seq according to the PIPseq 3’ T20 version 4.0 (Fluent Biosciences, now Illumina) protocol.

treatment_protocol: Tamoxifen injection to activate Cre recombinase under Lrig1 driver.

value: Small intestine

tag: genotype

tag: treatment

value: Tmx D5


title: RNA-seq of single blastomere (1cell_E09_B1)

description: Library name: 1cell_E09_B1

value: blastomerer derived from IVF


title: Uterus Transplant 3_Biopsy 2_L4_GEX

description:
Library name: UTx03Bx02CITE_S56_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: RNA

value: Endometrium

value: CD45+ Cells


title: Uterus Transplant 3_Biopsy 2_L2_ADT

description:
Library name: UTx03Bx02FB_S57_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: XX

value: Uterus Transplant


title: Day 5 Lrig1-G519R 2

description:
Library name: 12076_3
PIP-seq T-20 V.4


title: RNA-seq of single blastomere (1cell_E05_B1)

description: Library name: 1cell_E05_B1


title: Uterus Transplant 3_Biopsy 2_L3_GEX

description:
Library name: UTx03Bx02CITE_S56_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: TBM, blood,  MPH018, D56

description: Library name: DAV1202A109

value: Blood

tag: patient id

tag: study

value: laser

value: male

value: soc

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: Uterus Transplant 3_Biopsy 2_L2_GEX

description:
Library name: UTx03Bx02CITE_S56_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

tag: adt

tag: tissue


title: Day 3 Lrig1-G519R 2

description:
Library name: 12076_1
PIP-seq T-20 V.4

value: Tmx D3


title: RNA-seq of single blastomere (1cell_E03_B1)

description: Library name: 1cell_E03_B1


title: Day 3 Lrig1 M5B 2

description:
Library name: 12076_2
PIP-seq T-20 V.4


title: TBM, blood,  NSH012, D56

description: Library name: DAV1202A108

tag: timepoint

tag: age

tag: Sex

tag: antibiotics

tag: aspirin

value: no

tag: diagnosis

value: possible

value: negative


title: Uterus Transplant 3_Biopsy 2_L1_GEX

description:
Library name: UTx03Bx02CITE_S56_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: TotalSeq™-B Human Universal Cocktail v.1

tag: cell type

tag: genotype


title: RNA-seq of single blastomere (1cell_E02_B1)

description: Library name: 1cell_E02_B1

tag: Stage

tag: embryo id

tag: blastomere id


title: TBM, blood,  NSH008, D0

description: Library name: DAV1202A106

tag: patient id

tag: study

value: female

value: definite

tag: gxpu

value: positive

tag: mtb culture

tag: hiv vl


title: TBM, blood,  LH011, D7

description: Library name: DAV1202A107

tag: tissue

tag: blood wcc

tag: blood neutrophils


title: Uterus Transplant 1_Biopsy 4_L2_8_ADT

description:
Library name: UTx01Bx04_40-FB4_S23_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: ADT

tag: adt

tag: treatment


title: Day 5 Control 2

description:
Library name: 10785_4
PIP-seq T-20 V.4

value: Small intestine

value: Tmx D5


title: Uterus Transplant 1_Biopsy 4_L1_8_ADT

description:
Library name: UTx01Bx04_40-FB4_S23_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: Endometrium

value: CD45+ Cells

value: XX


title: Day 5 Lrig1-G519R 1

description:
Library name: 10785_3
PIP-seq T-20 V.4


title: TBM, blood,  MPH032, D7

description: Library name: DAV1202A105

value: Blood

value: laser

tag: timepoint

tag: age

tag: Sex

tag: antibiotics

tag: aspirin

tag: diagnosis


title: TBM, blood,  MPH022, D56

description: Library name: DAV1202A104

tag: patient id

value: male

value: soc


title: RNA-seq of single blastomere (1cell_E04_B1)

description: Library name: 1cell_E04_B1

tag: cell type

value: blastomerer derived from IVF

tag: Stage

tag: embryo id

tag: blastomere id


title: Day 3 Control 2

description:
Library name: 10785_2
PIP-seq T-20 V.4

tag: tissue

tag: genotype

value: Tmx D3


title: invitro_B6WT_1

city: Schlieren

first: Umesh

last: Ghoshdastider

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

description:
Library name: invitro_B6WT_1
Amplicon sequencing of genomic DNA after 10 passages of in vitro validation secondary screen in wildtype keratinocytes
FVF_invitro.csv

data_processing:
Bioinformatic analysis of single-cell RNA sequencing data: Raw sequencing data, consisting of BCL files, were demultiplexed using Illumina bcl2fastq v2.20 with default settings. One mismatch in the sample barcode sequences was allowed. The resulting fastq files were processed using the BD Rhapsody Pipeline (version 1.9.1) hosted at the Seven Brigdge’s cloud platform (https://www.sevenbridges.com/). A custom mouse reference genome, based on Gencode vM25 (GRCm38.p6), was generated and combined with the 720 sgRNAs sequences. Based on STAR aligner, a custom STAR reference genome was created and the Refined Putative Cell Calling option was disabled during the pipeline execution. For downstream analysis, unique molecular identifier (UMI) count data was corrected using BD Genomics Recursive Substitution Error Correction (RSEC). Processing PCR sgRNA dial-out data PCR dial-out data was processed using an in-house custom Python script as previously described (15). Three 9-nucleotide cell barcodes were extracted from the 97 possible barcodes from Read 1. One mismatch was allowed per barcode (Hamming distance of 1). The script also retrieved the 8-nucleotide UMI sequences from Read 1, as specified in the BD manual. For valid barcodes, sgRNAs were identified in Readd 2 by performing an exact match search for the 20-nucleotide sgRNA sequence. UMI counts per cell were deduplicated and sgRNA UMI counts per cell were computed. If multiple sgRNAs were detected for one cell, the cell was assigned to a specific sgRNA only if its UMI count exceeded the 99th percentile. Processing of single-cell RNA sequencing data The Scrublet Python package was used to remove doublets from each dataset separately. Genes expressed in a minimum of 5 cells were retained and an expected double rate of 20% (as estimated by BD Rhapsody) was applied. After filtering, seven P4 single-cell RNA-seq datasets and eight P60 datasets were merged using Seurat. Only cells containing detected sgRNAs and classified as singlets were selected for further analysis. Cells were filtered based on the following criteria: UMI counts > 500, UMI counts lower than the 0.99 quantile (to remove outliers) and mitochondrial gene content < 20%. Filtered datasets were then processed using Seurat’s standard pipeline. Gene expression was normalized using the NormalizeData function, which scales counts to 10,000 per cell followed by a natural log transformation (log1p). The FindVariableGenes function identified 2,000 highly variable genes, and data scaling was performed using ScaleData. Principal Component Analysis (PCA) was conducted with RunPCA and the ElbowPlot function was used to determine the top principal components that contributed to explaining the variance of the data for each dataset at P4 and P60. The FindNeighbors function was applied to identify nearest neighbors based in the selected principal components. Clustering was performed using FindClusters with Louvain modularity optimization. To visualize the data in two dimensions, UMAP (Uniform Manifold Approximation and Projection) was used. No batch effects were observed in the P4 and P60 datasets, so batch effect correction was not performed.
Assembly: Gencode Mouse vM25 (GRCm38.p6)
Supplementary files format and content: Comma-separated value files and matrix files with count numbers, *_counts.csv.gz files contain Cell Barcode, Gene Symbol and RSEC adjusted counts.

molecule: other

growth_protocol: All mice were housed at the Laboratory Animal Services Center (LASC) of the University of Zurich in individually-ventilated cages in a humidity- and light-controlled environment (22˚C, 45-50%, 12 h light/dark cycle), and had access to food and water ad libitum.

extract_protocol:
P4 back skin was processed as previously described (15). Fat was scraped off and the back skin was washed once in cold PBS and then placed in dispase (Corning #354235) dermis-side facing down, incubated for 35 min at 37 °C on an orbital shaker. Next, epidermis was separated from dermis with fine forceps and placed in 4 ml 0.25% Trypsin-EDTA (1×, Gibco; 25200056) for 15 min at 37 °C with orbital shaking. Epidermis was torn into smaller pieces and washed with cold PBS, pipetted vigorously up and down to achieve a single-cell suspension. Suspension was filtered through a 70-µm and subsequently a 40-µm strainer (Corning; #431750, #431751). Suspension was then centrifuged for 10 min at 400 g and resuspended in FACS buffer (PBS + 2% chelexed FBS (FBS(-)) + DAPI). P60 back skin was processed as previously described (15). Back skin was harvested with surgical scissors and placed dermis-facing up on a styrofoam rack with pins. Fat was scraped off with a scalpel. Fat-free skin was then washed, dermis-side facing down in 1× PBS. Skin was then placed in the same orientation in 0.5% Trypsin-EDTA (10×, Gibco; 15400054) and incubated at 37 °C on an orbital shaker for 25 min (females) or 50 min (males). Using a glass microscopy slide, skin was secured to the bottom of the dish and scraped again with a scalpel until it started to diverge. Excess cold PBS with 2% FBS(-) was added to neutralize trypsin. Cell suspension was strained on ice first through a 70-µm strainer, washed with an additional 15 ml of cold 1× PBS with 2% FBS (-) and then filtered through a 40-µm strainer. Cell suspension was spun down at 400 g for 10 min and resuspended in FACS buffer. P4: a total of 18 injected P4 mice were collected and assessed in 7 independent single-cell RNA sequencing runs. P60: a total of 7 injected mice were collected and assessed in 8 independent single-cell RNA sequencing runs.
Library construction protocol for scRNA-seq: EGFP-positive cells were sorted on a BD FACSAria III using a 70-µm nozzle and processed for single-cell capture with a BD Rhapsody Single-Cell Analysis System using BD Rhapsody Cartridge Kit (#633733). For P4, 7 separate cartridges with an average of 76,613 cells were loaded. For P60, 8 cartridges with an average of 68,171 cells were loaded. Reverse transcription from beads and sequencing library production was carried out according to the manufacturer’s instructions (BD Biosciences, doc ID: 210967 rev. 1.0). Library construction protocol for RNA-seq: RNA was isolated from lysates from nontargeting control and Gm10076 C7 keratinocytes as described in the Ribosome profiling section using TRIzol®  LS Reagent (Invitrogen, 10296028) and column purified with a Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared and sequenced at Novogene. Library construction protocol for Other:  As previously described, the sgRNA-containing region was amplified from the BD Rhapsody beads using a nested KAPA Polymerase reaction. In the first polymerase reaction (PCR1), the Rhapsody beads from each separate cartridges were resuspended and distributed into 4 separate 50 µL reactions  (100 µl KAPA HiFi HotStart ReadyMix (Roche 07958935001), 6 µl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 6 µl reverse primer (5′-TCTTGTGGAAAGGACGA-3′, 10 μM), 12 μl Bead RT/PCR Enhancer reagent from BD Biosciences and 72 μl nuclease-free water for a total volume of 200 μl). PCR1 conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 25 cycles of denaturation 95 °C for 30 s, annealing 53 °C for 30 s, extension 72 °C for 20 s and a final extension of 10 min at 72 °C. The 4 x 50 µl PCR1 product was pooled, and beads were removed using a magnet. Amplicons were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instructions. 3 μl of cleaned up PCR1 was used as template for PCR 2 (25 µL KAPA HiFi HotStart Ready Mix, 2 μl forward primer (5′-ACACGACGCTCTTCCGATCT-3′, 10 μM), 2 μl reverse primer (CAGACGTGTGCTCTTCCGATCTCTTGTGGAAAGGACGAAACA*C*C*G-3′, 10 μM), 18 μl nuclease-free water) for a total volume of 50 μl. PCR2 conditions were as follows: initial denaturation at 95 °C for 3 min, followed by 10 cycles of denaturation 95 °C for 30 s, annealing 60 °C for 3 min, extension 72 °C for 60 s, and a final extension of 5 min at 72 °C. Agencourt AMPure XP beads were used to clean up PCR2 product according to the manufacturer’s instructions  before the indexing PCR. Indexing PCR was performed according to BD Biosciences ‘mRNA Targeted Library Preparation’ protocol (doc ID: 210968 rev. 3.0). Library construction protocol for Ribo-seq: Ribosome profiling was conducted with some adjustments of the original method (64, 65). For RNA digestion, cell lysates were incubated with 1 U/µg of RNase 1 (Epicentre/Lucigen, 10U/µL) for 45 minutes at room temperature. Reaction was stopped by adding 4 µL of SUPERase Inhibitor (20 U/µL, SUPERase-InTM RNase Inhibitor Thermo Scientific AM2694). To eliminate free nucleotides and isolate ribosome-protected fragments, the RNase I-treated samples were processed using Amersham MicroSpin S-400 HR columns (Cytiva, 27514001). RNA extraction was performed utilizing TRIzol® LS Reagent (Invitrogen 10296028) in combination with the Direct-zolTM RNA MiniPrep kit (Zymo Research, R2052). Total RNA concentration was measured using QubitTM RNA broad range kit (Invitrogen, Q10210). Ribosome footprints were excised and extracted from a 15% TBE-UREA gel (Invitrogen, EC68852BOX) using the 20nt, 22nt, 27nt, 30nt and 60nt oligonucleotides mix as markers (1 µL of 10 µM dilution in 19µL RNase-free H2O). Extraction was performed overnight with RNA extraction buffer (300mM NaOAc pH=5.5, 1mM EDTA, 0.25% v/v SDS). T4 PNK (NEB, M0201S) end-healing reaction was performed on the ribosome footprints for 1 hour at 37˚C. Linker ligation reaction followed using T4 RnI truncated K227Q (NEB, M0351L) in combination with 20 µM of preadenylated linker for 3 hours at 22˚C (50% w/v PEG-8000, 10X T4 RNA ligase, preadenylated linker, T4 RnI truncated K227Q). Ribosomal RNA was depleted using biotinylated rRNA depletion oligos (2 µM) by mixing 10 µL of sample with 10 µL of oligo mix and incubated for 2 minutes at 80˚C, followed by a gradual decrease in temperature to 25˚C. MyOne Streptavidin dynabeads (Life Technologies, 65001) were used to recover the samples. Reverse transcription was performed on the Ribosomal RNA-free samples using SuperScriptTM IV Reverse Transcriptase (Invitrogen, 18090050). Footprints were excised and extracted from a 15% TBE-UREA gel. Extraction was performed overnight with DNA extraction buffer (10mM Tris-HCl pH=8, 300mM NaCl, 1mM EDTA). cDNA was circularized using CircLigase II (100 U/µL, Biosearch, CL4115K) for 1 hour at 60˚C. cDNA was amplified using Phusion High-Fidelity DNA polymerase (Thermo Scientific, F530S) using an individual index per sample. 6-12 cycle amplicons were visualized using an 8% TBE non-denaturing polyacrylamide gel to determine optimal cycle number. PCR was carried out with 7-9 cycles and analyzed on an 8% TBE non-denaturing polyacrylamide gel (Invitrogen, EC61252BOX). DNA was excised from gel and extracted using DNA extraction buffer by incubating overnight with gentle shaking. DNA was recovered and precipitated in 10 mM Tris-HCl pH=8. DNA was quantified using Qubit TM 1X dsDNA High Sensitivity Assay (Invitrogen, Q33230) and quality was verified using the Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626). Samples were pooled and prepared for sequencing.

tag: cell line

value: Keratinocytes


title: Uterus Transplant 1_Biopsy 4_L2_7_ADT

description:
Library name: UTx01Bx04_39-FB3_S7_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: TotalSeq™-B Human Universal Cocktail v.1

value: Uterus Transplant


title: invitro_B6WT_2

description:
Library name: invitro_B6WT_2
Amplicon sequencing of genomic DNA after 10 passages of in vitro validation secondary screen in wildtype keratinocytes
FVF_invitro.csv


title: Day 3 Lrig1-G519R 1

description:
Library name: 10785_1
PIP-seq T-20 V.4


title: Uterus Transplant 1_Biopsy 4_L1_7_ADT

description:
Library name: UTx01Bx04_39-FB3_S7_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: adt


title: TBM, blood,  NSH012, D7

description: Library name: DAV1202A103

tag: study

value: no

value: possible

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: TBM, blood,  GSH004, D0

description: Library name: DAV1202A102

tag: timepoint

tag: age

tag: Sex

tag: antibiotics

value: intensified

tag: aspirin

tag: diagnosis


title: invitro_Pik3ca_1

description:
Library name: invitro_Pik3ca_1
Amplicon sequencing of genomic DNA after 10 passages of in vitro validation secondary screen in Pik3ca keratinocytes
FVF_invitro.csv

source_name: Pik3ca (H1047R)

value: Pik3ca (H1047R)

tag: cell type


title: Day 5 Control 1

description:
Library name: 10395_3
PIP-seq T-20 V.4

tag: tissue

value: Small intestine

tag: genotype

tag: treatment

value: Non treated


title: TBM, blood,  MPH022, D0

description: Library name: DAV1202A100

tag: patient id

value: definite

value: positive


title: Day 3 Lrig1 M5B 1

description:
Library name: 10395_2
PIP-seq T-20 V.4


title: TBM, blood,  MPH013, D56

description: Library name: DAV1202A101

value: Blood

tag: study

value: laser

value: female

value: probable


title: invitro_Pik3ca_2

description:
Library name: invitro_Pik3ca_2
Amplicon sequencing of genomic DNA after 10 passages of in vitro validation secondary screen in Pik3ca keratinocytes
FVF_invitro.csv

tag: cell line


title: Uterus Transplant 1_Biopsy 4_L2_6_ADT

description:
Library name: UTx01Bx04_38_S18_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: ADT

tag: adt

value: Endometrium

value: CD45+ Cells

value: XX


title: Uterus Transplant 1_Biopsy 4_L2_5_ADT

description:
Library name: UTx01Bx04_37-FB1_S8_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: TotalSeq™-B Human Universal Cocktail v.1

value: Uterus Transplant


title: Day 5 Lrig1 M5B 1

description:
Library name: 10395_4
PIP-seq T-20 V.4

value: Tmx D5


title: TBM, blood,  NSH016, D7

description: Library name: DAV1202A99

value: soc

value: no

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Uterus Transplant 1_Biopsy 4_L1_5_ADT

description:
Library name: UTx01Bx04_37-FB1_S8_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes


title: invitro_Hras_1

description:
Library name: invitro_Hras_1
Amplicon sequencing of genomic DNA after 10 passages of in vitro validation secondary screen in Hras SCC cells
FVF_invitro.csv

source_name: Hras Tgfbr null (SCC)

value: Hras Tgfbr null (SCC)

value: Keratinocytes


title: Uterus Transplant 1_Biopsy 4_L1_6_ADT

description:
Library name: UTx01Bx04_38_S18_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes


title: RNA-seq of single blastomere (1cell_E01_B1)

description: Library name: 1cell_E01_B1

value: blastomerer derived from IVF

tag: Stage

tag: embryo id

tag: blastomere id


title: Liver, PmlKO, rep1.

description: Library name: PmlKO

data_processing:
scRNA-seq reads were first processed with 10×Genomics Cell Ranger (v7.2.0). Cells with fewer than 200 unique genes, fewer than 500 transcripts or more than 10% mitochondrial reads were filtered. Seurat package (v5.1.0) was used for further processing, cell clustering, and downstream analysis.
Assembly: hg38
Supplementary files format and content: tsv files of CellRanger filtered matrix

source_name: Liver

extract_protocol:
Liver tissues from Pmlfl/fl, PmlLSECKO mice were perfused according to the protocol of LSEC isolation to obtain single cell suspension. Then cells were centrifuged at 50 g for 5 minutes to remove hepatocytes. The collected suspension was centrifuged at 300 g for 10 minutes to obtain cell pellet, which was washed twice and resuspended in cold PBS with 0.04% BSA. Then cells were counted using a hemocytometer. After counting the cells, 10,000 cells were decided as the appropriate target volume for each sample. The samples were then loaded onto the 10x Genomics single-cell-A chip.
After single-cell suspension was prepared, the following steps were execuded following the Chromium Single Cell 3’ Reagent v3 user guide. In brief, droplets were generated with the single cells and barcoded beads, after which cDNA synthesis was performed. The droplets were broken, then cDNA was amplified and libraries were constructed. Finally, the single-cell libraries were sequenced on the Illumina platform.

treatment_protocol: Pml flox/flox mice were crossed with Cdh5CreERT2 mice to generate Pmlflox/flox/Cdh5CreERT2 mice. These mice at 6-7 weeks old were intraperitoneally injected with tamoxifen (75 mg/kg/day) for 5 consecutive days to induce LSEC-specific Pml (PmlLSECKO) knockout.

value: Liver

value: Pml LSECKO


title: TsixStop Rep2, Input, NPCd3

status: Public on Mar 12 2026

city: Oxford

first: Mafalda

last: Almeida

address: South Parks Rd

department: Biochemistry

institute: University of Oxford

description: Library name: nC0766_TsixStop_NPCd3_Input_Rep2

data_processing:
ChIP-sequencing analysis was performed using previously established pipelines45. For calibrated ChIP-seq experiments, raw fastq reads were mapped using Bowtie2 (v.2.3.5.1)67 to the 129S1xCast N-masked mm10 genome concatenated with the dm6 Drosophila genome using the following parameters: “--very-sensitive --no-discordant --no-mixed -X 2000”. Unmapped reads were then removed. PCR duplicates were identified and removed using picard-tools “MarkDuplicates” (Broad Institute) and remaining reads were then assigned to each allele using SNPsplit68. To calculate calibration factors, mm10 and dm6 mapped reads for each sample and input were counted using SAMtools (v.1.16)69. Calibration factors for cChIP-seq were then calculated according to the derived formula for occupancy ratio (ORi)70. In order to generate calibrated bigwig files for mouse chrX, bam files were initially filtered using the “intersect” function from BEDtools (v.2.30.0)71 to generate a bam file containing mouse chrX reads only. During the generation of the iXist-ChrXCast cell line using CRISPR-Cas9–facilitated homology-directed recombination, two SNPs (mm10, chrX:103482682 A/T and mm10, chrX:103482895 A/T) between the Cast and 129 alleles became uninformative, as both X alleles were converted to the 129 allele (T at both positions). Consequently, any reads spanning these two sites are no longer allele-specific as intended and were therefore removed from the allelic BAM files. BAM files were then sorted and indexed using SAMtools69 and bigWig files were finally generated using deepTools (v.3.5.1)72 bamCoverage per 10 million reads considering the calibration factors. BigWig files were then visualized using IGV (https://software.broadinstitute.org/software/igv/)73. To quantify the number of ChIP reads per kb over the Xist locus (chrX: 103460373-103483233), we used the function “bigWigAverageOverBed” from UCSCTools.
Assembly: mm10; dm6
Supplementary files format and content: bigWig

source_name: Tsix Stop on 129 allele leading to non-random X inactivation upon differentiation

growth_protocol: mESC were grown in ESC medium at 37oC in a 5% CO2 incubator and passaged onto 0.1% gelatin-coated plates in feeder-dependent conditions every 2-3 days using TrypLE Express (Life Technologies). Mitomycin C-inactivated SNLP (STO mouse fibroblasts expressing Neomycin and Puromycin resistance and Lif genes) were used as feeder cells. Cells were pre-plated and passaged at least twice to remove feeders prior to cell collection for genomic experiments. ESC medium consisted of Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS), 1x NEAA (Non-essential amino acids; Life Technologies), 2mM L-glutamine (Life Technologies), 1x Penicillin-Streptomycin (Life Technologies), 50µM b-mercaptoethanol (Life Technologies) and Leukemia Inhibitory Factor (LIF)-conditioned medium made in-house. Mouse embryonic stem cells were differentiated into NPC as previously described62,63. To obtain feederless mESC cell suspensions, mESC were collected using TrypLE and pre-plated four consecutive times for 40 min each. Cells were then washed in PBS twice to remove any traces of FBS and counted using a Countess® II FL Automated Cell Counter (Life Technologies). Cells were then resuspended in N2B27 medium (50% Neurobasal; 50% DMEM/F12 with 0.5x N2 and 0.25x B27, 1mM L-glutamine, 0.5x Penicillin-Streptomycin, 100μM b-mercaptoethanol, all from Life Technologies) supplemented with 1μg/mL of doxycycline to induce Xist expression simultaneously with the onset of differentiation, and plated at a density of 20,000 cells per cm2 in pre-gelatinized plates. Cells were fed daily from day 2 to day 7 of differentiation and fed also on day 1 for experiments in which this corresponded to the timepoint of 100 nM dTAG-13 addition. dTAG-13 treated NPC cultures were fed with media containing dTAG-13 from NPCd1 onwards until collection. On day 7, cells were dissociated by incubation with accutase (diluted 1:3 in PBS) (Merck Life Sciences) and counted. Three million cells were resuspended in N2B27 supplemented with doxycycline and 10 ng/mL EGF (cat# 315-09, Peprotech) and 10 ng/mL FGF2 (cat# 100-18B, Peprotech) and plated to grow in suspension in non-adherent bacterial petri dishes to promote embryoid body formation. On day 10, cells were recovered by centrifugation and plated onto pre-gelatinized dishes to expand more homogeneous neural stem cell cultures. At this point, neural stem cells were fed every other day and passaged as required using accutase (diluted 1:3 in PBS) (Merck Life Sciences) until the required timepoint. Cells were collected for different experiments at the appropriate timepoints (generally, NPCd1, d3 and d7 for ChIP experiments and multiple timepoints from NPCd1 to NPCd28 for chromatin-RNA) by washing with PBS and then incubating the cells at room temperature with accutase (diluted 1:3 in PBS) (Merck Life Sciences) until they were dissociated for collection.

extract_protocol:
Calibrated native ChIP-seq (cChIP-seq) was performed for H3K9me3 by collecting 5x107 mESCs or NPCs and spiking in 1 × 107 Drosophila Sg4 cells counted using a Countess II FL Automated Cell Counter (Life Technologies). Cells were pelleted by centrifugation and resuspended in 1mL of cold RSB (10mM Tris pH 8.0, 10mM NaCl, 3mM MgCl2) and lysed by addition of 14mL of cold RSB supplemented with 0.1% NP40 and gentle inversion. Nuclei were recovered by centrifugation at 1500 x g for 5 min at 4oC and washed in 4ml RSB with 0.25M sucrose and 3mM CaCl2 supplemented with protease inhibitors. Nuclei were recovered by centrifugation at 1500 x g for 5 min at 4oC and resuspended in 1mL of RSB with 0.25M sucrose and 3mM CaCl2 supplemented with protease inhibitors, which was transferred to a 1.5mL tube for MNase digestion (200U, Fermentas EN0181) of chromatin to mono- and di-nucleosomes at 37oC for 5 min with inversion every minute. The reaction was quenched by addition of 8µL 0.5M EDTA and spun at 5,000rpm for 5min at 4oC. The supernatant (S1) was collected into a new 1.5mL tube and kept on ice. The pellet was thoroughly resuspended in 300µL of Nucleosome Release Buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2mM EDTA) supplemented with protease inhibitors, and incubated for 1hour at 4oC with rotation. This suspension was passed five times through a 27G needle using a 1mL syringe and then spun at 5000rpm for 5min at 4oC. The supernatant (S2) was collected and combined with S1. The chromatin was centrifuged at 13000rpm for 5min to remove any precipitant, and supernatant was collected as chromatin, snap frozen and stored at -80oC until further processing. For immunoprecipitation (IP), chromatin was thawed on ice and 110µL were diluted in 1mL of native ChIP incubation buffer (70mM NaCl, 10mM Tris pH 7.5, 2mM MgCl2, 2mM EDTA, 0.1% Triton X-100) freshly supplemented with protease inhibitors.  100µL were transferred to a new 1.5mL tube and stored at 4oC to be used as input. The remaining diluted chromatin was incubated overnight with rotation with 5µg of H3K9me3 antibody (Abcam, ab8898) or H3K9me3 (Active Motif; AB2532132 Clone 0319; Cat #061013). Samples were then incubated for 90min with 45µL rProtein A Sepharose™ Fast Flow beads (Amersham) pre-blocked with 1mg/mL of yeast tRNA and 1mg/mL BSA. The beads were then washed five times for 10min with rotation at 4oC with Wash Buffer (20mM Tris pH 7.5, 2mM EDTA, 125mM NaCl, 0.1% Triton X-100) followed by one final wash in 1x TE. The DNA was then eluted from the beads by incubation at 25oC for 30 min shaking at 1000rpm with 1% SDS, 100 mM NaHCO3 elution buffer and separated from the beads by centrifugation. DNA from the IP elutions and input samples was further purified using the ChIP DNA Clean and Concentrator Kit (Zymo Research) according to manufacturer’s instructions.
ChIP and input DNA was quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and submitted to library preparation using the the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Libraries were quantified using the Qubit High Sensitivity DNA kit (Invitrogen) and their length was estimated using the Bioanalyzer High Sensitivity DNA kit (Agilent) before pooling and subjected to paired-end sequencing on an Illumina NextSeq 500 machine using NextSeq 500/550 High-Output v2.5 Kit (150 cycles) (Illumina).

treatment_protocol: To induce Xist expression, medium was supplemented with 1µg/mL doxycycline. To induce protein degradation in lines expressing FKBP12F36V-tagged proteins, medium was supplemented with 100nM dTAG-13 (Tocris Bioscience).

tag: strain background

value: Cast x 129S

value: NPC

tag: chip antibody

tag: spike-in

value: spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: FVF_DO19

description:
Library name: FVF_DO19
dial-out nested PCR for sgRNA amplification for P60 secondary validation library

source_name: mouse epidermis

tag: tissue

value: mouse epidermis

tag: cell type

value: skin cells

tag: genotype

value: Pik3ca x LSLCas9


title: Uterus Transplant 1_Biopsy 4_L2_4_GEX

description:
Library name: UTx01Bx04_36_S11_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: RNA

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

tag: treatment


title: FVF_WTA19

description:
Library name: FVF_WTA19
scRNA-seq WTA of P60 skin, CROP-seq-CRE P60 secondary validation library


title: TBM, blood,  GSH006, D0

description: Library name: DAV1202A97

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

tag: age

tag: Sex

value: male

tag: antibiotics

value: intensified

tag: aspirin

value: yes

tag: diagnosis

value: definite

value: positive

tag: blood neutrophils


title: TBM, blood,  MPH027, D14

description: Library name: DAV1202A98

value: female

value: soc

value: no

value: possible

tag: gxpu

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Liver, CCl4, rep1.

description: Library name: CCl4

tag: tissue

value: Liver

value: Pml fl/fl


title: FVF_DO18

description:
Library name: FVF_DO18
dial-out nested PCR for sgRNA amplification for P4 for secondary validation library

value: mouse epidermis

tag: cell type

value: skin cells

value: Pik3ca x LSLCas9


title: Uterus Transplant 1_Biopsy 4_L1_4_GEX

description:
Library name: UTx01Bx04_36_S11_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

tag: genotype

value: XX

value: Uterus Transplant


title: Uterus Transplant 1_Biopsy 4_L2_3_GEX

description:
Library name: UTx01Bx04_34_S24_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: treatment


title: Liver, OliveOil, rep1.

description: Library name: OliveOil

value: olive oil


title: Uterus Transplant 1_Biopsy 4_L1_3_GEX

description:
Library name: UTx01Bx04_34_S24_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: Day 3 Control 1

description:
Library name: 10395_1
PIP-seq T-20 V.4

value: Small intestine

value: Tmx D3


title: TBM, blood,  MPH037, D7

description: Library name: DAV1202A95

value: Blood

tag: patient id

tag: study

value: laser

tag: timepoint

value: male

value: intensified

value: yes

value: definite

value: positive


title: Liver, Brd4KO, rep3

description: Library name: Brd4KO_3

data_processing:
scRNA-seq reads were first processed with 10×Genomics Cell Ranger (v7.2.0). Cells with fewer than 200 unique genes, fewer than 500 transcripts or more than 10% mitochondrial reads were filtered. Seurat package (v5.1.0) was used for further processing, cell clustering, and downstream analysis.
Assembly: hg38
Supplementary files format and content: tsv,mtx files of CellRanger filtered matrix

extract_protocol:
Liver tissues from Brd4fl/fl, Brd4LSECKO mice were perfused according to the protocol of LSEC isolation to obtain single cell suspension. Then cells were centrifuged at 50 g for 5 minutes to remove hepatocytes. The collected suspension was centrifuged at 300 g for 10 minutes to obtain cell pellet, which was washed twice and resuspended in cold PBS with 0.04% BSA. Then cells were counted using a hemocytometer. After counting the cells, 10,000 cells were decided as the appropriate target volume for each sample. The samples were then loaded onto the 10x Genomics single-cell-A chip.
After single-cell suspension was prepared, the following steps were execuded following the Chromium Single Cell 3’ Reagent v3 user guide. In brief, droplets were generated with the single cells and barcoded beads, after which cDNA synthesis was performed. The droplets were broken, then cDNA was amplified and libraries were constructed. Finally, the single-cell libraries were sequenced on the Illumina platform.

treatment_protocol: Brd4flox/flox mice were crossed with Cdh5CreERT2 mice to generate Brd4flox/flox/Cdh5CreERT2 mice. These mice at 6-7 weeks old were intraperitoneally injected with tamoxifen (75 mg/kg/day) for 5 consecutive days to induce LSEC-specific Brd4 (Brd4LSECKO) knockout.

value: Liver

value: Brd4 LSECKO


title: TBM, blood,  NSH014, D0

description: Library name: DAV1202A96

tag: age

tag: Sex

tag: antibiotics


title: Liver, Brd4KO, rep2

description: Library name: Brd4KO_2


title: TBM, blood,  MPH002, D14

description: Library name: DAV1202A94

value: female

tag: aspirin

value: no

tag: diagnosis

value: possible

value: negative

tag: blood neutrophils


title: Uterus Transplant 1_Biopsy 4_L2_2_GEX

description:
Library name: UTx01Bx04_34_S14_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: RNA

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

value: Uterus Transplant


title: lib_sec_S1

description:
Library name: lib_sec_S1
Amplicon sequencing T0 secondary library Replicate 2 to verify sgRNA representation
FVF_invitro.csv

source_name: plasmid library

value: plasmid library


title: Metaphocytes,csf1ra-/-b-/-, wt, 3dpf, fli1a- mpeg+, plate2

city: Utrecht

first: Catherine

last: Robin

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: Metaphocytes_csf1rab, plate2
Metaphocytes, GFP+ Cherry-, sorted from the trunk of csf1ra-/-b-/- 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

data_processing:
Library preparation was done following the CEL-Seq2 protocol (Hashimshony et al. (2016) Genome Biol.
Assembly: danio rerio Zv9
Supplementary files format and content: matrix files

organism: Danio rerio

source_name: trunk

growth_protocol: sort-Seq on zebrafish embryos 3 dpf

extract_protocol:
Embryos were collected and anesthetized in E3 medium containing 0.01% tricaine and placed in ice-cold PBS. After centrifugation, the pellet was washed with ice-cold PBS and resuspended in TrypLE (ThermoFisher, 12563011) for 45 min at 32°C with vigorous shaking. Cells were then washed with FACS buffer (PBS + 2% FBS + 2mM EDTA), dissolved in FACS buffer supplemented with DAPI (ThermoFisher, 0.5 mg/ml final concentration) and subsequently filtered through 40-μm nylon mesh. Cells were sorted on a FACS Aria II (BD Biosciences)
384 plates were processed by Single Cell Discoveries using the SORT-seq protocol (Muraro, M. J. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst. 3, 385-394.e3 (2016)). Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform.

value: trunk

value: Metaphocytes


title: Liver, Brd4KO, rep1

description: Library name: Brd4KO_1


title: Liver, CCl4, rep3

description: Library name: CCl4_3

value: Brd4 fl/fl


title: lib_sec_S2

description:
Library name: lib_sec_S2
Amplicon sequencing T0 secondary library Replicate 2 to verify sgRNA representation
FVF_invitro.csv


title: TBM, blood,  NSH020, D7

description: Library name: DAV1202A93

value: Blood

value: laser

value: male

value: intensified

tag: gxpu

tag: mtb culture

tag: hiv vl


title: TBM, blood,  GSH009, D0

description: Library name: DAV1202A92

tag: tissue

value: female

value: no

value: probable

tag: blood wcc


title: bMs, csf1ra-/-b-/-, 3dpf, fli1a+ mpeg+, plate2

description:
Library name: bMs_csf1rab, plate2
bMs, GFP+ Cherry+, sorted from the trunk of csf1ra-/-b-/- 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

tag: cell type

value: bMs


title: invitro_Hras_2

description:
Library name: invitro_Hras_2
Amplicon sequencing of genomic DNA after 10 passages of in vitro validation secondary screen in Hras SCC cells
FVF_invitro.csv

tag: cell line

value: Hras Tgfbr null (SCC)

value: Keratinocytes

tag: genotype


title: Uterus Transplant 1_Biopsy 4_L1_2_GEX

description:
Library name: UTx01Bx04_34_S14_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

tag: treatment


title: Uterus Transplant 1_Biopsy 4_L2_1_GEX

description:
Library name: UTx01Bx04_33_S13_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: XX

value: Uterus Transplant


title: Uterus Transplant 1_Biopsy 4_L1_1_GEX

description:
Library name: UTx01Bx04_33_S13_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: TBM, blood,  NSH002, D7

description: Library name: DAV1202A90

tag: patient id

tag: study

tag: timepoint

tag: age

value: yes

value: negative


title: Uterus Transplant 1_Biopsy 3_L4_ADT

description:
Library name: UTx01_Bx03_CS_csp_S48_L004
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: ADT


title: Liver, CCl4, rep2

description: Library name: CCl4_2

value: Liver

value: Brd4 fl/fl


title: TBM, blood,  MPH022, D7

description: Library name: DAV1202A89

value: Blood

value: laser

tag: Sex

value: male

tag: antibiotics

value: soc

tag: aspirin

tag: diagnosis

value: definite

value: positive


title: Macrophages, wt, 3dpf, fli1a- mpeg+, plate2

description:
Library name: Macrophages_wt, plate2
Macrophages, GFP+ Cherry-, sorted from the trunk of wt 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

value: trunk

value: Macrophages

value: wildtype


title: Liver, OliveOil, rep3

description: Library name: OliveOil_3

value: olive oil


title: Liver, CCl4, rep1

description: Library name: CCl4_1


title: Uterus Transplant 1_Biopsy 3_L3_ADT

description:
Library name: UTx01_Bx03_CS_csp_S48_L003
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX


title: Uterus Transplant 1_Biopsy 3_L2_ADT

description:
Library name: UTx01_Bx03_CS_csp_S48_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: ADT

value: Uterus Transplant


title: Metaphocytes,csf1ra-/-b-/-, wt, 3dpf, fli1a- mpeg+, plate1

description:
Library name: Metaphocytes_csf1rab, plate1
Metaphocytes, GFP+ Cherry-, sorted from the trunk of csf1ra-/-b-/- 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

value: Metaphocytes


title: Liver, OliveOil, rep2

description: Library name: OliveOil_2

value: Liver

value: Brd4 fl/fl


title: Liver, OliveOil, rep1

description: Library name: OliveOil_1


title: Neutrophils, wt, 3dpf, mpx+, plate2

description:
Library name: Neutrophils_wt, plate2
Neutrophils, GFP+, sorted from the trunk of wt 3 dpf Tg(mpx:GFP)

value: Neutrophils


title: Uterus Transplant 1_Biopsy 3_L1_ADT

description:
Library name: UTx01_Bx03_CS_csp_S48_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes


title: TBM, blood,  MPH037, D14

description: Library name: DAV1202A88

value: Blood

value: laser

value: male

value: intensified

value: yes

tag: gxpu

tag: mtb culture

value: negative

tag: hiv vl

tag: blood neutrophils


title: TBM, blood,  GSH006, D7

description: Library name: DAV1202A87

tag: tissue

value: definite

value: positive

tag: blood wcc


title: bMs, wt, 3dpf, fli1a+ mpeg+, plate2

description:
Library name: bMs_wt, plate2
bMs, GFP+ Cherry+, sorted from the trunk of wt 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

value: trunk

tag: cell type

value: bMs

tag: genotype

value: wildtype


title: old, 5-week

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

description:
Library name: 5W_old
10x Genomics

data_processing:
We processed the raw FASTQ sequencing files using CellRanger 6.1.1 with alignment to the 10x Genomics human reference genome (refdata-gex-mm10-2020-A). We imported the filtered count matrices into Seurat v5, and assigned each cell a unique identifier to prevent overlap of barcodes between different samples. We normalized, log-transformed, and scaled the count matrices to remove unwanted sources of variation such as discrepancies in sequencing depth. We identified the top 2000 highly variable genes for principal component analysis. We integrated across samples to account for any sample- or experiment-specific batch effects using the Harmony package. We utilized these harmony embeddings to run Uniform Manifold Approximation and Projection dimensional reduction to 2 dimensions. We clustered cells according to the Louvain algorithm and identified marker genes for each cluster using Wilcoxon rank sum tests comparing each cluster to all other clusters.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: EAU.RDS: Seurat object containing processed and merged data. Sample-level metadata is provided in metadata slots ('timepoint_age').

source_name: retina

extract_protocol:
We pooled retinas and digested tissue in papain solution (125 units/ml) containing protease & phosphatase inhibitor and DNAse I (5,000 units/ml). After 40 min digestion at 4C, we neutralized the reaction using ovomucoid solution. Then, we enriched the single cell suspension for CD45-positive cells using the EasySep Mouse CD45 Positive Selection Kit following the manufacturer's recommended protocol. Finally, we washed and re-suspended the cells in DMEM media containing 10% fetal bovine serum and used them as input for single cell RNA sequencing on the 10x Genomics platform.
We used the Chromium Single Cell 3’v3.1 Reagent Kit according to the manufacturer's protocol.

treatment_protocol: We used young (6-7 weeks old) and aged (92-93 weeks old) male C57BL/6J mice for the experimental autoimmune mouse model of uveitis (EAU) as described previously. Briefly, we administered to each mouse by subcutaneous injection 300 micrograms human interphotoreceptor retinoid-binding protein peptide (sequence 651-670, LAQGAYRTAVDLESLASQLT) emulsified in Complete Freund's adjuvant containing 5 mg/ml M. tuberculosis strain H37Ra. We also administered intraperitoneally to each mouse 0.5 ug Bordetella pertussis toxin (5 ug/ml in PBS). At 2- and 5-weeks after immunization, we sacrificed mice and dissected eyes to obtain neural retinas.

value: retina

tag: pooled mice_(n)

tag: treatment

value: experimental autoimmune uveitis

value: 5 week

value: 93 week


title: bMs, csf1ra-/-b-/-, 3dpf, fli1a+ mpeg+, plate1

description:
Library name: bMs_csf1rab, plate1
bMs, GFP+ Cherry+, sorted from the trunk of csf1ra-/-b-/- 3 dpf Tg(fli1a:laCherry; mpeg:GFP)


title: Uterus Transplant 1_Biopsy 3_L4_GEX

description:
Library name: UTx01_Bx03_CS_3p_S27_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

value: Uterus Transplant


title: Neutrophils, wt, 3dpf, mpx+, plate1

description:
Library name: Neutrophils_wt, plate1
Neutrophils, GFP+, sorted from the trunk of wt 3 dpf Tg(mpx:GFP)

value: Neutrophils


title: old, 2-week

description:
Library name: 2W_old
10x Genomics

value: male

tag: timepoint

tag: age

value: 92 week


title: Macrophages, wt, 3dpf, fli1a- mpeg+, plate1

description:
Library name: Macrophages_wt, plate1
Macrophages, GFP+ Cherry-, sorted from the trunk of wt 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

value: Macrophages


title: Uterus Transplant 1_Biopsy 3_L3_GEX

description:
Library name: UTx01_Bx03_CS_3p_S27_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads


title: TBM, blood,  LH010, D0

description: Library name: DAV1202A83

value: Blood

tag: patient id

tag: study

value: laser

tag: Sex

value: female

tag: antibiotics

value: intensified

value: no

value: possible

value: negative


title: bMs, wt, 3dpf, fli1a+ mpeg+, plate1

description:
Library name: bMs_wt, plate1
bMs, GFP+ Cherry+, sorted from the trunk of wt 3 dpf Tg(fli1a:laCherry; mpeg:GFP)

value: trunk

value: bMs

value: wildtype


title: TBM, blood,  LH011, D0

description: Library name: DAV1202A84

value: soc

tag: aspirin

tag: diagnosis

value: definite

tag: gxpu

value: positive

tag: mtb culture


title: young, 5-week

description:
Library name: 5W_young
10x Genomics

tag: tissue

value: retina

value: experimental autoimmune uveitis

value: 2 week

value: 7 week


title: Uterus Transplant 1_Biopsy 3_L1_GEX

description:
Library name: UTx01_Bx03_CS_3p_S27_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: RNA

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

tag: cell type

value: CD45+ Cells

value: XX

value: Uterus Transplant


title: Uterus Transplant 1_Biopsy 3_L2_GEX

description:
Library name: UTx01_Bx03_CS_3p_S27_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: genotype


title: TBM, blood,  GSH002, D14

description: Library name: DAV1202A85

value: Blood

value: laser

value: male

value: no

value: possible

value: negative

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: TBM, blood,  NSH011, D7

description: Library name: DAV1202A86

value: intensified

value: definite

value: positive


title: young, 2-week

description:
Library name: 2W_young
10x Genomics

value: retina

tag: pooled mice_(n)

tag: treatment

value: experimental autoimmune uveitis

value: 2 week

value: 6 week


title: TBM, blood,  LH007, D14

description: Library name: DAV1202A82

tag: timepoint

tag: age


title: CTCF_larvae_CTCFdeltaCP_SuHwdelta114_PitadeltaCP1_1

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

description: Library name: Sample_45

data_processing:
Trimming Illumina adapters with cutadapt
Trimming low quality tails with sickle (https://github.com/najoshi/sickle) (with -q 20 option)
Alignment with bowtie2 against version dm6 of the Drosophila melanogaster genome
Filtration of PCR duplicates and non-unique mapping with picard (https://broadinstitute.github.io/picard/)
Blacklist filtration with bedtools
Reproducible peaks calling was conducted against corresponding preimmune controls with IDR pipeline (https://sites.google.com/site/anshulkundaje/projects/idr).  A soft p value threshold for MACS2 in IDR of 0.01, the IDR reproducibility threshold was set to 0.05 for true replicates and 0.01 for pseudoreplicates. All samples showed good reproducibility (the rescue ratio or/and the self consistency ratio were <2).
ChiP-Seq coverage tracks were obtained using deepTools (Ramírez et al. 2014) bamCoverage functions  with a bin width of 50 bps and RPKM normalization.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by IDR and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Drosophila strains were maintained on standard medium at 25°C and 50-60% humidity.

extract_protocol:
After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted using a ChIP DNA Clean &Concentrator kit (Zymo Research, USA).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with MagSelect XP beads (Magen). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on aNovaSeq 6000 (Illumina) in pair-end mode.

treatment_protocol: Chromatin was prepared from third-instar larvae. 500 milligrams of larvae was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, and 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized in a Potter and Dounce homogenizer with a tight pestle, filtered through a 100 µm Nylon Cell Strainer (Miltenyi Biotec, USA), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, and protease inhibitors) and one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, and protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, and protease inhibitors). The suspension of nuclei was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test the extent of sonication and measure the DNA concentration. Debris was removed by centrifugation at 14,000 x g, 4°C, for 10 min, and chromatin was pre-cleared with Protein G Dynabeads (Invitrogen, USA). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein G (rat anti-CP190, 1:300; rat anti-Su(Hw), 1:200; rat non-specific IgG) or Protein A (rabbit anti-HA, 1:500; rabbit anti-Pita, 1:200; rabbit non-specific IgG) Dynabeads (Thermo Fisher Scientific, USA) mixed with 200 µL of PBST. Then antibody–Dynabead complexes were washed and equilibrated in nuclear lysis buffer. Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL nuclear lysis buffer (2 µL aliquots of pre-cleared chromatin as input material) were incubated overnight at 4°C with antibody–Dynabead complexes.

value: whole organism

tag: development stage

value: larvae

tag: antibody source

value: rabbit

tag: strain

tag: antibody

value: dCTCF (HA)


title: Healthy Control 20_L3_GEX

description:
Library name: HC20_S12_L003
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

value: Healthy Control


title: p55-GN11-NP50ug-mL-24h-pellet

city: Milan

first: Anna

last: Cariboni

address: Via Balzaretti 9

department: Disfeb

country: Italy

institute: Università degli Studi di Milano

description: Library name: Sample 5

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
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
The gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: GRCm38
Supplementary files format and content: csv file include TPM values for each Sample

growth_protocol: GN11 cells were maintained in DMEM high-glucose supplemented with 10% FBS, 2mM L-glutamine and antibiotics in humified atmosphere at 37°C with 5% CO2

extract_protocol:
Total RNA was extracted from frozen cell pellet samples using Qiagen RNeasy Mini kit following manufacturer’s instructions (Qiagen)
RNA sequencing library preparation used NEBNext Ultra II RNA Library Prep Kit for Illumina. Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented according to manufacturer’s instruction. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies), and quantified by using Qubit 4.0 Fluorometer (Invitrogen).

treatment_protocol: 50ug/mL 500nm polystyrene nanoplastic for 24h

tag: cell line

value: immortalized GnRH neurons

value: wild type

tag: batch


title: TBM, blood,  NSH019, D0

description: Library name: DAV1202A79

tag: tissue

value: Blood

tag: patient id

tag: study

value: laser

tag: Sex

value: female

tag: antibiotics

value: intensified

tag: aspirin

value: yes

tag: diagnosis

value: definite

tag: gxpu

value: positive

tag: mtb culture

value: negative


title: p54-GN11-NP50ug-mL-24h

description: Library name: Sample 4

tag: cell type

tag: genotype

tag: treatment

value: 50ug/mL 500nm polystyrene nanoplastic for 24h


title: TBM, blood,  MPH001, D56

description: Library name: DAV1202A80

tag: timepoint

tag: age

value: male

value: soc

value: no

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: CTCF_larvae_CTCFdeltaCP_PitadeltaCP1_4

description: Library name: Sample_42

tag: tissue

value: whole organism

tag: development stage

value: larvae

tag: antibody source

value: rabbit

tag: strain

tag: antibody

value: dCTCF (HA)


title: CTCF_larvae_CTCFdeltaCP_SuHwdelta114_PitadeltaCP1_2

description: Library name: Sample_46


title: Healthy Control 20_L2_GEX

description:
Library name: HC20_S12_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

value: Healthy Control


title: GN11-p39-1mln-pellet

description: Library name: Sample 2

tag: cell line

value: immortalized GnRH neurons

value: wild type

value: untreated

tag: batch


title: GN11-p40-1mln-pellet

description: Library name: Sample 3

tag: cell type


title: TBM, blood,  NSH018, D14

description: Library name: DAV1202A78

value: Blood

tag: patient id

tag: study

value: laser

tag: Sex

tag: antibiotics

value: intensified

tag: aspirin

value: yes

tag: diagnosis

value: possible

tag: gxpu

value: negative

tag: mtb culture


title: CTCF_larvae_CTCFdeltaCP_PitadeltaCP1_3

description: Library name: Sample_41

tag: tissue

value: whole organism

tag: genotype

tag: development stage

value: larvae

value: rabbit


title: Healthy Control 20_L1_GEX

description:
Library name: HC20_S12_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

value: RNA

value: TotalSeq™-B Human Universal Cocktail v.1

tag: treatment


title: TBM, blood,  NSH018, D7

description: Library name: DAV1202A77

tag: timepoint

tag: age

value: male

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: CP190_larvae_CTCFdeltaCP_SuHwdelta114_PitadeltaCP1_2

description: Library name: Sample_44

tag: antibody source

value: rat

tag: strain

tag: antibody


title: Healthy Control 20_L4_GEX

description:
Library name: HC20_S12_L004
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

tag: adt

value: Endometrium

tag: cell type

value: CD45+ Cells

value: XX

value: Healthy Control


title: Healthy Control 20_L4_ADT

description:
Library name: HC20-FB_S13_L004
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

value: ADT


title: TBM, blood,  MPH016, D14

description: Library name: DAV1202A76

value: Blood

tag: patient id

tag: study

value: laser

tag: Sex

value: female

tag: antibiotics

value: soc

tag: aspirin

value: no

tag: diagnosis

value: probable

tag: gxpu


title: CP190_larvae_CTCFdeltaCP_SuHwdelta114_PitadeltaCP1_1

description: Library name: Sample_43

tag: tissue

value: whole organism

tag: genotype

tag: development stage

value: larvae


title: Healthy Control 20_L3_ADT

description:
Library name: HC20-FB_S13_L003
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: treatment


title: Healthy Control 20_L2_ADT

description:
Library name: HC20-FB_S13_L002
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes


title: GN11-p38-pellet

description: Library name: Sample 1

tag: cell line

value: immortalized GnRH neurons

value: wild type

value: untreated

tag: batch


title: CTCF_larvae_CTCFdeltaCP_PitadeltaCP1_1

description: Library name: Sample_39

tag: antibody source

value: rabbit

tag: strain

tag: antibody

value: dCTCF (HA)


title: CTCF_larvae_CTCFdeltaCP_PitadeltaCP1_2

description: Library name: Sample_40


title: FVF_DO17

description:
Library name: FVF_DO17
dial-out nested PCR for sgRNA amplification for P60 secondary validation library

value: mouse epidermis

tag: cell type

value: skin cells

value: Pik3ca x LSLCas9


title: TBM, blood,  MPH015, D0

description: Library name: DAV1202A81

tag: patient id

tag: timepoint

tag: age

value: male

value: intensified

value: yes

value: negative

tag: mtb culture

tag: hiv vl

tag: blood wcc

tag: blood neutrophils


title: FVF_DO16

description:
Library name: FVF_DO16
dial-out nested PCR for sgRNA amplification for P60

tag: tissue


title: CP190_larvae_CTCFdeltaCP_PitadeltaCP1_4

description: Library name: Sample_38

tag: genotype

value: rat


title: TBM, blood,  NSH015, D14

description: Library name: DAV1202A75

value: Blood

tag: study

value: laser

tag: Sex

tag: antibiotics

tag: aspirin

value: no

tag: diagnosis

value: possible

tag: gxpu


title: p56-GN11-NP50ug-mL-24h-pellet

description: Library name: Sample 6

tag: cell line

value: immortalized GnRH neurons

tag: treatment

value: 50ug/mL 500nm polystyrene nanoplastic for 24h

tag: batch


title: CP190_larvae_CTCFdeltaCP_PitadeltaCP1_3

description: Library name: Sample_37

value: whole organism

tag: development stage

value: larvae

tag: antibody source

tag: strain

tag: antibody


title: TBM, blood,  MPH001, D7

description: Library name: DAV1202A73

tag: patient id

tag: timepoint

tag: age

value: soc

value: definite

value: positive

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: Healthy Control 12_L2_GEX

description:
Library name: HC12-GEX_S3_L002
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: library type

value: RNA

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

tag: tissue

value: Endometrium

tag: cell type

value: CD45+ Cells

tag: genotype

value: XX

value: Healthy Control


title: FVF_DO15

description:
Library name: FVF_DO15
dial-out nested PCR for sgRNA amplification for P60

value: mouse epidermis

value: skin cells

value: Pik3ca x LSLCas9


title: FVF_DO14

description:
Library name: FVF_DO14
dial-out nested PCR for sgRNA amplification for P60


title: Healthy Control 12_L1_GEX

description:
Library name: HC12-GEX_S3_L001
10x Genomics, GEX 3' Library: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains transcripts/sequence reads

tag: treatment


title: TBM, blood,  GSH011, D7

description: Library name: DAV1202A72

value: Blood

tag: study

value: laser

tag: Sex

value: male

tag: antibiotics

value: intensified

tag: aspirin

value: no

tag: diagnosis

value: probable

tag: gxpu

value: negative

tag: blood neutrophils


title: CP190_larvae_CTCFdeltaCP_PitadeltaCP1_2

description: Library name: Sample_36

value: whole organism

tag: development stage

value: larvae

tag: antibody source

value: rat

tag: strain

tag: antibody


title: TBM, blood,  MPH036, D0

description: Library name: DAV1202A74

tag: patient id

tag: timepoint

tag: age

value: yes

value: definite

value: positive

tag: mtb culture

tag: hiv vl

tag: blood wcc


title: FVF_DO12

description:
Library name: FVF_DO12
dial-out nested PCR for sgRNA amplification for P4

tag: tissue

tag: cell type

tag: genotype


title: CTCF_larvae_CTCFdeltaCP_SuHwdelta114_4

description: Library name: Sample_34

value: rabbit

value: dCTCF (HA)


title: TBM, blood,  MPH027, D0

description: Library name: DAV1202A70

tag: study

tag: Sex

value: female

tag: antibiotics

value: soc

tag: aspirin

value: possible


title: Healthy Control 12_L1_ADT

description:
Library name: HC12-FB_S9_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: ADT

tag: adt

value: TotalSeq™-B Human Universal Cocktail v.1

value: Endometrium

value: CD45+ Cells

value: XX

tag: treatment

value: Healthy Control


title: CP190_larvae_CTCFdeltaCP_PitadeltaCP1_1

description: Library name: Sample_35

value: whole organism

tag: development stage

tag: antibody source

tag: strain

tag: antibody


title: Healthy Control 20_L1_ADT

description:
Library name: HC20-FB_S13_L001
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes


title: TBM, blood,  MPH016, D56

description: Library name: DAV1202A69

value: Blood

tag: patient id

value: laser

tag: timepoint

tag: age

value: no

tag: diagnosis

value: probable

tag: gxpu

value: negative

tag: mtb culture

tag: blood neutrophils


title: FVF_DO13

description:
Library name: FVF_DO13
dial-out nested PCR for sgRNA amplification for P60

tag: tissue

value: mouse epidermis

tag: cell type

value: skin cells

tag: genotype

value: Pik3ca x LSLCas9


title: CTCF_larvae_CTCFdeltaCP_SuHwdelta114_3

description: Library name: Sample_33

value: larvae

value: rabbit

value: dCTCF (HA)


title: Healthy Control 10_L4_ADT

description:
Library name: HC10_CS_csp_S16_L004
ADT: Read 1 file contains cell barcodes and Unique Molecular Identifiers (UMI); Read 2 file contains antibody derived tags/barcodes

tag: library type

value: ADT

value: TotalSeq™-B Human Universal Cocktail v.1


title: CTCF_larvae_CTCFdeltaCP_SuHwdelta114_2

description: Library name: Sample_32


title: TBM, blood,  GSH005, D7

description: Library name: DAV1202A68

tag: study

tag: Sex

value: male

tag: antibiotics

value: intensified

tag: aspirin

tag: hiv vl

tag: blood wcc


title: FVF_DO11

description:
Library name: FVF_DO11
dial-out nested PCR for sgRNA amplification for P4


title: TBM, blood,  GSH006, D14

description: Library name: DAV1202A71

tag: patient id

value: yes

value: definite

value: positive


title: CTCF_larvae_CTCFdeltaCP_SuHwdelta114_1

description: Library name: Sample_31

value: whole organism

tag: development stage

tag: antibody source

tag: strain

tag: antibody