title: MNaseSeq_ESC_cecr2_ko_B_rep1

value: tip5 knock-out


title: NSLA_585

status: Public on Mar 11 2024

type: SRA

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

country: South Korea

institute: KRIBB

library_source: transcriptomic

data_processing:
STAR mapping (2.9.10) with GeneCount function Assembly: GRCh38 Supplementary files format and content: Genecounts as text formats
Assembly: GRCh38
Supplementary files format and content: txt

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.
We used the TruSeq DNA Library Prep Kit (Illumina, San Diego, CA, USA) for TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) for stranded total RNA-seq library, following the manufacturer’s instructions. For paired-end sequencing was performed using an Illumina NovaSeq 6000 sequencing instrument, the constructed library was sequenced using a HiSeq 4000 sequencing system, resulting in 2× 100 bp sequencing reads.

tag: tissue

value: Lung

tag: subject status

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

tag: cell type

value: NSCLC

tag: Stage

tag: age

tag: gender

value: FEMALE


title: CD4 Met 1

city: Tel Aviv

first: Neta

last: Erez

address: TAU

department: Pathology

country: Israel

institute: Tel Aviv University

data_processing:
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1
Sequencing data was then trimmed using fastp 0.20.0 and aligned to the GRCm38 assembly using STAR 2.6.0c
DESeq2 1.30.1 and R 3.6 were used for normalization of count data and for statistical analysis of differential gene expression.
Assembly: Reads were mapped to the Mus musculus genome (mm10) using STAR.
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Bone metastatic lesion

extract_protocol:
EZ-RNA Total RNA Isolation Kit
MARS-seq protocol was used to generate libraries

value: Bone metastatic lesion

value: CD4+ T helper

tag: treatment

value: Late met stage


title: MNaseSeq_ESC_bptf_ko_A_rep3

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. MNase-seq reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig

molecule: genomic DNA

source_name: embryonic stem cells

extract_protocol:
DNA was purified using AMPure XP beads
Sequencing libraries were prepared from 500ng of MNase digested DNA using the NEBNext Ultra Library Preparation Kit (NEB) with 5 PCR amplification cycles.

value: embryonic stem cells

tag: cell line

tag: genotype


title: MNaseSeq_ESC_acf1_ko_C_rep2

value: wt


title: MNaseSeq_ESC_bptf_ko_A_rep2

value: rsf1 knock-out


title: NSLA_571


title: MNaseSeq_ESC_bptf_ko_A_rep1


title: NSLA_581


title: CD4 Periph 3

source_name: bone marrow

value: bone marrow


title: MNaseSeq_ESC_acf1_ko_C_rep1


title: MNaseSeq_ESC_wstf_ko_A_rep1


title: B6_Foxn1Cre_Nfe2l2_flox_mTEC_RNA_rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

data_processing:
For non-F1-hybrid RNA-seq, paired-end RNA-seq reads were aligned to the mm10 genome using STAR. Non-uniquely mapped reads were discarded. The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25). TPM (Transcripts Per Million) values for genes were output by Kallisto (‘quant’, v0.45.1).
For F1-hybrid RNA-seq experiments, quality control was performed using Sickle (default setting, v1.33) to remove low-quality reads. Paired-end RNA-seq reads were aligned to the corresponding reference or alternative genome using Tophat2 (v2.1.1). Only paired-end reads mapped to the single unique genomic location were kept for downstream analysis (SAMtools, v1.3.1).
Assembly: mm10 and NOD/ShiLtJ
Supplementary files format and content: *kallisto.tsv: output file of kallisto 'quant' function
Supplementary files format and content: *genes_count.tsv: gene count table

source_name: Thymus

extract_protocol:
For each sample, 1000 cells were sorted directly into the lysis buffer [5uL TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma)]. Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

treatment_protocol: mTECs were isolated by collagenase and dispase digestion, CD45+ cells depletion using magnetic beads, fluorescent antibodies staining, and flow sorting.

value: Thymus

value: mTEChi

value: Foxn1-cre,Nfe2l2 fl/fl

value: 4-6 weeks old

tag: Sex

value: Female

tag: strain


title: B6_Foxn1Cre_Nfe2l2_flox_mTEC_RNA_rep1


title: NSLA_563


title: B6_Foxn1Cre_Nfe2l2_wt_mTEC_RNA_rep2


title: NSLA_595


title: NSLA_56


title: CD4 Periph 2


title: B6_Foxn1Cre_Nfe2l2_wt_mTEC_RNA_rep1


title: CD4 Periph 1


title: B6_Topotecan_WT_mTEC_RNA_rep2

value: WT

value: Topotecan ip injection


title: B6_Topotecan_WT_mTEC_RNA_rep1


title: NSLA_543

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations


title: NSLA_555

value: NSCLC

value: FEMALE


title: CD4 Premet 4

value: CD4+ T helper

value: Early met stage


title: B6_DMSO_WT_mTEC_RNA_rep1

value: DMSO ip injection


title: CD4 Periph 4

value: Late met stage


title: CD4 Premet 3


title: B6_DMSO_WT_mTEC_RNA_rep2


title: NSLA_542


title: B6_PBS_WT_mTEC_RNA_rep1

value: PBS ip injection


title: CD4 Premet 1

value: bone marrow


title: NOD_Aire_KO_mTEC_GFP_RNA_rep2

value: Thymus

value: Aire-GFP+ mTECs

value: Aire-KO

value: NOD/ShiLtJ


title: B6_PBS_Aire_KO_mTEC_RNA_rep2

value: mTEChi

value: 4-6 weeks old

value: Female


title: CD4 Normal 4

value: Normal


title: B6_Spermidine_WT_mTEC_RNA_rep2

value: WT

value: Spermidine ip injection


title: CD4 Premet 2


title: NSLA_535

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

value: FEMALE


title: B6_Spermidine_WT_mTEC_RNA_rep1


title: NSLA_519


title: CD4 Normal 3

value: CD4+ T helper


title: B6_PBS_Aire_KO_mTEC_RNA_rep1

value: PBS ip injection


title: NOD_Aire_KO_mTEC_GFP_RNA_rep3


title: NSLA_540


title: CD4 Normal 2

value: bone marrow


title: NSLA_541


title: B6_PBS_WT_mTEC_RNA_rep2

value: Thymus


title: NOD_Aire_KO_mTEC_GFP_RNA_rep1

value: Aire-GFP+ mTECs


title: NSLA_50


title: NSLA_490


title: CD4 Normal 1


title: NOD_WT_mTEC_GFP_RNA_rep1


title: B6_Aire_KO_mTEC_GFP_RNA_rep2

value: Aire-KO


title: Granulocytes Met 3

value: Granulocyte

value: Late met stage


title: NSLA_488


title: NOD_WT_mTEC_GFP_RNA_rep3

value: 4-6 weeks old

value: NOD/ShiLtJ


title: B6_Spermidine_Aire_KO_mTEC_RNA_rep2

value: mTEChi

value: Female


title: B6_Spermidine_Aire_KO_mTEC_RNA_rep1

value: Spermidine ip injection


title: Granulocytes Met 1


title: B6_WT_mTEC_GFP_RNA_rep2

value: WT


title: B6_WT_mTEC_GFP_RNA_rep3


title: NSLA_479

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations


title: B6_NOD_F1_WT_mTEC_GFP_RNA_rep2

value: C57BL/6J and NOD/ShiLtJ F1


title: Granulocytes Periph 3


title: IgG_CutTag_rep1

data_processing:
Low-quality reads were removed using Sickle and adapter sequences were trimmed using cutadapt (v1.14).
Reads were aligned to the corresponding genome by bowtie2 (v2.3.4.3) with the following parameters: --local --very-sensitive --no-mixed --no-discordant -X 1000 –fr. Reads were aligned to the E. coli genome in parallel to quantify the number of carry-over reads from pA-Tn5.
Non-uniquely mapped and mitochondrial DNA reads were removed using a combination of SAMtools functions.
PCR duplicates were removed using Picard (‘MarkDuplicates’, v2.8.0).
Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10
Supplementary files format and content: *.bw: bigwig files
Library strategy: CUT&Tag

extract_protocol:
Cells were washed in wash buffer 1 (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine, Complete EDTA-free protease inhibitor cocktail). After washing, cells were bound to the Concanavalin A beads (Bangs Laboratories), followed by incubation with 1:50 primary antibody in wash buffer 1 supplemented with 0.05% digitonin, 2mM EDTA and 0.1% BSA at 4°C overnight. The next day, cells were incubated with 1:100 secondary antibody in wash buffer 1 supplemented with 0.05% digitonin at room temperature for 1 h on a rotator. After washing, cells were mixed with 1:200 pA-Tn5 (124601, Addgene; purified in-house) in wash buffer 2 (20mM HEPES pH 7.5, 300mM NaCl, 0.5mM spermidine, Complete EDTA-free protease inhibitor cocktail) plus 0.01% digitonin at room temperature for 1 h on a rotator. Cells were then washed twice, followed by tagmentation in wash buffer 2 plus 0.01% digitonin and 10mM MgCl2 at 37°C for 1 h. DNA was solubilized by adding 16.7mM EDTA, 0.1% SDS and 0.167mg/mL Proteinase K to each sample and incubating at 55°C for 1 h. DNA was phenol-chloroform extracted.
Libraries were indexed and amplified using the NEBNext High-Fidelity 2x PCR Master Mix (M0541S, NEB) and ATAC-seq primers, followed by purification using AMPure XP beads.

tag: cut&tag antibody

value: guinea pig anti-rabbit IgG (611-201-122, Rockland)


title: NSLA_483

value: NSCLC

value: FEMALE


title: B6_Aire_KO_mTEC_GFP_RNA_rep1

value: Thymus


title: NOD_WT_mTEC_GFP_RNA_rep2

value: Aire-GFP+ mTECs


title: Granulocytes Met 2

value: bone marrow


title: Granulocytes Periph 4

value: Granulocyte


title: Aire_KO_PolII_pS5_CutTag_rep2

value: anti-RNA polymerase II phospho S5 (ab5131, abcam)

value: Aire-KO


title: Aire_KO_PolII_pS5_CutTag_rep1

value: 4-6 weeks old


title: Granulocytes Periph 1

value: Late met stage


title: B6_NOD_F1_WT_mTEC_GFP_RNA_rep3

value: Female


title: B6_WT_mTEC_GFP_RNA_rep1


title: Granulocytes Periph 2


title: Input_Chipmentation_for_Aire_rep1

data_processing:
Low-quality reads were removed using Sickle and adapter sequences were trimmed using cutadapt (v1.14).
Reads were aligned to the corresponding genome by bowtie2 (v2.3.4.3) with the following parameters: -X 1000 --fr --no-mixed --no-discordant.
Non-uniquely mapped and mitochondrial DNA reads were removed using a combination of SAMtools functions.
PCR duplicates were removed using Picard (‘MarkDuplicates’, v2.8.0).
Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10
Supplementary files format and content: *.bw: bigwig files
Library strategy: ChIPmentation

extract_protocol:
Cells were fixed with 1% formaldehyde (28906, Thermo Fisher Scientific) for 10 min at room temperature with rotation, followed by quenching using 0.125M glycine for 5 min at room temperature. After washing using ice-cold PBS supplemented with protease inhibitor (Complete EDTA-free protease inhibitor cocktail, Roche), cells were resuspended in lysis buffer (10mM Tris-HCl pH 8.0, 140mM NaCl, 1mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) supplemented with protease inhibitor on ice for 10 min. Chromatin was then sonicated on the Covaris M220 ultrasonicator with the following settings: peak incident power 50, duty factor 10%, cycles per burst 200, time 5 min. Lysate was centrifuged for 10 min at 14,000g at 4°C. An “input” sample was preserved from the supernatant. The rest of the supernatant was incubated with 2 ug of anti-Aire (14-5934-82, eBioscience) or anti-NELF (ab170104, abcam) antibody precoupled to Protein A Dynabeads (Invitrogen) on a rotator overnight at 4°C. On the following day, beads were washed twice sequentially on a pre-cold magnet (Invitrogen) using wash buffer 1 (10mM Tris-HCl pH 8.0, 140mM NaCl, 1mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100), wash buffer 2 (10mM Tris-HCl pH 8.0, 500mM NaCl, 1mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100), wash buffer 3 (10mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate) and 10mM Tris-HCl pH 8.0. Beads were then resuspended in 25uL tagmentation reaction mix with 1uL Tn5 transposase (Illumina) added, and were incubated at 37°C for 5 min. After removing the tagmentation reaction mix, beads were washed twice with wash buffer 1 and once with 1 x TE. They were then incubated with 50uL elution buffer (10mM Tris-HCl pH 8.0, 300mM NaCl, 5mM EDTA, 0.4% SDS) containing 2uL Proteinase K (NEB) at 55°C for 1h and 65°C for 8h to de-crosslink. DNA was purified using MinElute Reaction Cleanup Kit (QIAGEN).
Libraries were indexed and amplified using the NEBNext High-Fidelity 2x PCR Master Mix (M0541S, NEB) and ATAC-seq primers, followed by purification using AMPure XP beads.

value: mTEChi

tag: chipmentation antibody

value: Topotecan ip injection


title: Granulocytes Premet 4

value: Early met stage


title: NSLA_469

value: Lung

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations


title: NSLA_460


title: WT_Topotecan_Aire_Chipmentation_rep2

value: anti-Aire (14-5934-82, eBioscience)

value: WT


title: NSLA_464

value: NSCLC

value: FEMALE


title: B6_NOD_F1_WT_mTEC_GFP_RNA_rep1

value: Thymus

value: Aire-GFP+ mTECs

value: C57BL/6J and NOD/ShiLtJ F1


title: NSLA_475


title: NSLA_471


title: WT_DMSO_Aire_Chipmentation_rep2

value: DMSO ip injection


title: Granulocytes Premet 2

value: bone marrow

value: Granulocyte


title: NSLA_459


title: WT_PolII_pS5_CutTag_rep1

value: anti-RNA polymerase II phospho S5 (ab5131, abcam)

value: 4-6 weeks old


title: WT_DMSO_Aire_Chipmentation_rep1

value: mTEChi

value: Female


title: Granulocytes Premet 1

value: Early met stage


title: WT_PolII_pS5_CutTag_rep2


title: NSLA_426

value: Lung


title: Aire_KO_NELF_Chipmentation_rep1

value: anti-NELF (ab170104, abcam)

value: Aire-KO


title: WT_NELF_Chipmentation_rep2

value: WT


title: NSLA_429

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: Input_Chipmentation_for_NELF_rep1

value: Thymus


title: WT_NELF_Chipmentation_rep1


title: WT_Spermidine_BLISS_rep1

data_processing:
Cutadapt (v2.5) was used to scan BLISS reads for matches of the expected 16bp prefix [8bp unique molecular identifier (UMI) + 8bp sample barcode] in the BLISS adapters, allowing a maximum of one mismatch. Only reads containing the 16bp prefix were kept. Prefixes were clipped using Cutadapt.
Reads were aligned to the corresponding genome using bowtie2 (v2.3.4.3). Only uniquely mapped reads were kept (SAMtools, v1.3.1).
PCR duplicates that had the same UMIs (allowing for a maximum of two mismatch) were removed using UMI-tools (‘dedup’, v1.0.1). DSBs independently generated at the same genomic location in different cells were kept because they had different UMIs.
Bam files were generated using SAMtools (v1.3.1). Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10 and CAST/EiJ
Supplementary files format and content: *.bw: bigwig files
Library strategy: Breaks Labeling In Situ and Sequencing (BLISS)

extract_protocol:
We followed the suspension-cell BLISS protocol. Cells were fixed in 4% paraformaldehyde (15710, Electron Microscopy Sciences) for 10 min at room temperature on a roller shaker. Formaldehyde was quenched with glycine. Fixed cells were then washed twice using ice-cold PBS. For permeabilization, fixed cells were subjected to two sequential lysis using lysis buffer 1 (10mM Tris-HCl, 10mM NaCl, 1mM EDTA, 0.2% Triton X-100, pH 8) and lysis buffer 2 (10mM Tris-HCl, 150mM NaCl, 1mM EDTA, 0.3% SDS, pH 8). After permeabilization, DSB ends were blunted using the Quick Blunting Kit (E1201L, NEB) for 1 h at room temperature, which was followed by in situ DSB ligation of BLISS adapters using T4 DNA ligase (M0202M, NEB) for ~16 h (overnight) at 16°C. On Day 2, genomic DNAs were reverse crosslinked and extracted using DNA extraction buffer (10mM Tris-HCl, 100mM NaCl, 50mM EDTA, 1% SDS, 1mg/mL Proteinase K, pH 8) at 55°C for ~18 h (overnight) with shaking. On Day 3, DNA was purified and then sonicated in 1 x TE buffer using the Covaris M220 ultrasonicator with the following setting: peak incident power 50, duty factor 10%, cycles per burst 200, time 70s. DNA was then purified by Agencourt AMPure XP beads. DNA was in vitro transcribed using the MEGAscript T7 Transcription Kit (AM1333, ThermoFisher) at 37°C for ~14 h (overnight). On Day 4, genomic DNA was removed using DNase I (RNase-free) (AM2222, ThermoFisher) followed by RNA purification using Agencourt RNAClean XP beads (Beckman Coulter).
Libraries were built via the following steps: Illumina RA3 adapter ligation using T4 RNA Ligase 2, truncated KQ (M0373S, NEB) at 25°C for 2 h; reverse transcription using SuperScript III Reverse Transcriptase (18080044, ThermoFisher) at 50°C for 1 h; library indexing and amplification using NEBNext High-Fidelity 2x PCR Master Mix (M0541S, NEB); DNA purification and size-selection (300-800bp) using Agencourt AMPure XP beads. All primers and adapters were custom synthesized by Integrated DNA Technologies (IDT) based on sequences in TruSeq Small RNA Library Preparation kit (Illumina).

value: Spermidine ip injection


title: Granulocytes Premet 3


title: Granulocytes Normal 4

value: Normal


title: NSLA_421

value: FEMALE


title: Granulocytes Normal 3

value: bone marrow


title: Aire_KO_NELF_Chipmentation_rep2


title: Granulocytes Normal 2

value: Granulocyte


title: WT_Spermidine_BLISS_rep2


title: WT_PBS_BLISS_rep1

value: PBS ip injection


title: NSLA_398


title: WT_Topotecan_BLISS_rep2

value: 4-6 weeks old

value: Topotecan ip injection


title: Granulocytes Normal 1


title: WT_Topotecan_Aire_Chipmentation_rep1

value: mTEChi

value: anti-Aire (14-5934-82, eBioscience)

value: Female


title: WT_Topotecan_BLISS_rep1


title: NSLA_382

value: Lung


title: WT_DMSO_BLISS_rep1

value: DMSO ip injection


title: iNKTcells, HTO-derived library

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline.
Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression).
Assembly: Alignments were performed using pre-build Cell Ranger mouse mm10 reference.
Supplementary files format and content: 10x Genomics output files are barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz. Stage 0 and Stage 3 NKT datasets were analyzed using Seurat. Seurat R objects are called nkt_stage0_final.rds and nkt_stage3_final.rds
Library strategy: scRNA-seq and CITE-seq

molecule: protein

extract_protocol:
To perform the single-cell RNA sequencing experiments, cells of 4 thymi of Ctrl mice were pooled and the same was done with 4 thymi of T-KO mice. Cells were stained with CD1d tetramers, anti-TCRβ, anti-NK1.1, anti-CD44 and anti-CD24 antibodies on ice. Cells were sorted by flow cytometry for TCRβ+, CD1dt+, CD24+, NK1.1- cells to obtain stage 0 iNKT cells, and for TCRβ+, CD1dt+, NK1.1+, CD24-, CD44+ cells to obtain stage 3 iNKT cells. This was done twice in parallel, to have two replicas each. After sorting, each cell population was barcoded by hash-tagged antibodies (TotalSeqC format, anti-mouse Hashtag 1 to 8; clone M1/42, 30-F11, BioLegend). The antibody concentrations used were 1 ug per million cells. After staining, cells were washed three times in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 x g 5 min at 4 °C) and supernatant exchange. Then all 8 populations were pooled (2x stage 0 Ctrl, 2x stage 0 T-KO, 2x stage 3 Ctrl, 2x stage 3 T-KO).
Single-cell RNA sequencing was performed using 10x Genomics with feature barcoding technology to multiplex cell samples from different mice well to reduce costs and minimize technical variability. Hashtag oligos were obtained as purified and already oligo-conjugated in TotalSeq-C (5’ chemistry) formats from BioLegend. Cells were stained with barcoded antibodies after sorting. Cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions. Libraries were pooled to desired quantities to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.

value: Invariant natural killer T cells

tag: library type

value: HTO

tag: antibodies/tags

value: TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody for Stage 0 iNKT from Ctrl 1 TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody for Stage 3 iNKT from Ctrl 1 TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody for Stage 0 iNKT from Ctrl 2 TotalSeq™-C0304 anti-mouse Hashtag 4 Antibody for Stage 3 iNKT from Ctrl 2 TotalSeq™-C0305 anti-mouse Hashtag 5 Antibody for Stage 0 iNKT from T-KO 1 TotalSeq™-C0306 anti-mouse Hashtag 6 Antibody for Stage 3 iNKT from T-KO 1 TotalSeq™-C0307 anti-mouse Hashtag 7 Antibody for Stage 0 iNKT from T-KO 2 TotalSeq™-C0308 anti-mouse Hashtag 8 Antibody for Stage 3 iNKT from T-KO 2


title: Aire_KO_BLISS_rep2

value: Thymus

value: Aire-KO


title: B6_CAST_F1_BLISS_rep1

value: WT

value: C57BL/6J and CAST/EiJ F1


title: ChIPseq_ESC_BPTF_input_BPTFko_rep1

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
Assembly: mm10
Supplementary files format and content: wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.

extract_protocol:
DNA was purified using AMPure XP beads
Sequencing libraries were prepared using the NEBNext Ultra II Library Preparation Kit (NEB) with 12 PCR amplification cycles for Ips and 6 PCR amplification cycles for inputs.

value: embryonic stem cells

value: Bptf knock-out


title: B6_CAST_F1_BLISS_rep2


title: WT_BLISS_rep2


title: iNKTcells, mRNA-derived library

description: poly A RNA

molecule: polyA RNA

value: mRNA


title: NSLA_379

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

value: FEMALE


title: WT_DMSO_BLISS_rep2

value: mTEChi

value: 4-6 weeks old


title: NSLA_380

value: Lung


title: B6_Spermidine_Aire_KO_mTEC_ATAC_rep2

data_processing:
Low-quality reads were removed using Sickle and adapter sequences were trimmed using cutadapt (v1.14).
Reads were aligned to the corresponding genome by bowtie2 (v2.3.4.3) with the following parameters: -X 1000 --fr --no-mixed --no-discordant.
Non-uniquely mapped and mitochondrial DNA reads were removed using a combination of SAMtools functions.
PCR duplicates were removed using Picard (‘MarkDuplicates’, v2.8.0).
Bam files were generated using SAMtools (v1.3.1). Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10 and NOD/ShiLtJ
Supplementary files format and content: *.bw: bigwig files

extract_protocol:
Cells were spun down at 4°C and washed with 1mL PBS supplemented with protease inhibitor (Complete EDTA-free protease inhibitor cocktail, Roche). Then 10uL Tn5 transposase mixture was added to resuspend the cell pellet on ice. [10uL Tn5 transposase mixture: 5uL 2x Tagment DNA Buffer, 0.5uL Tagment DNA Enzyme from the Nextera DNA Library Preparation Kit (Illumina), 4.4uL nuclease-free water, 0.2mg/ml digitonin (G9441, Promega)]. Cells were incubated for 30 min at 37°C with agitation. Transposed DNA fragments were purified using the MinElute Reaction Cleanup Kit (QIAGEN).
Two rounds of PCR were performed to generate the library as described in the ImmGen ATAC-seq protocol. After the initial round of PCR with 7 cycles, small DNA fragments were size-selected and purified using the Agencourt AMPure XP beads (Beckman Coulter) followed by a second round of PCR with 10 cycles. Amplified libraries were purified by AMPure XP beads (x1.8 vol.).

value: Female

value: Spermidine ip injection


title: B6_Spermidine_Aire_KO_mTEC_ATAC_rep1


title: WT_PBS_BLISS_rep2

value: PBS ip injection


title: NSLA_407


title: NSLA_377


title: Aire_KO_BLISS_rep1


title: WT_BLISS_rep1


title: NSLA_365


title: ChIPseq_ESC_BPTF_input_wt_rep2

value: wild-type


title: NSLA_374


title: ChIPseq_ESC_BPTF_input_wt_rep1


title: BSseq_XX_d2_r2

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

data_processing:
Adaptor and quality trimming was performed using Trim Galore (v0.6.4)
Reads were aligned to mm10 using BSMAPz.
.bam files were sorted with samtools (v1.10) and duplicate reads removed using Picard (v2.7.1)
.bedGraph files were generated using Methyldackel (v0.3.0) [extract –minDepth 2]
Lastly, blackliseted regions and mitochondrial reads were removed.
Assembly: mm10
Supplementary files format and content: .bedGraph files containing per-base CpG methylation (merged or biological replicates)

source_name: XX ESCs

growth_protocol: Cells were kept on gelatine, without feeders in 2i/LIF + Serum conditions.

extract_protocol:
gDNA extraction and bisulfite conversion
Whole-Genome Bissulfite sequencing

treatment_protocol: Cells were differentiated for the indicated days using 2i/LIF-withdrawal.

value: XX ESCs

value: TX1072 XXdXic

value: Cast x B6


title: B6_PBS_Aire_KO_mTEC_ATAC_rep2

value: Thymus

value: Aire-KO


title: B6_PBS_Aire_KO_mTEC_ATAC_rep1


title: NOD_WT_mTEC_GFP_ATAC_rep2

value: Aire-GFP+ mTECs

value: Aire-GFP+

value: NOD/ShiLtJ


title: ChIPseq_ESC_BPTF_IP_BPTFko_rep2

value: embryonic stem cells

value: Bptf knock-out


title: NSLA_362

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC

value: FEMALE


title: ChIPseq_ESC_BPTF_input_BPTFko_rep2


title: NOD_WT_mTEC_GFP_ATAC_rep1

value: 4-6 weeks old

value: Female


title: B6_WT_mTEC_GFP_ATAC_rep2


title: NSLA_356

value: Lung


title: B6_WT_mTEC_GFP_ATAC_rep1


title: ChIPseq_ESC_BPTF_IP_BPTFko_rep1


title: B6_NOD_F1_WT_mTEC_GFP_ATAC_rep2

value: C57BL/6J and NOD/ShiLtJ F1


title: ChIPseq_ESC_BPTF_IP_wt_rep2

value: wild-type


title: B6_NOD_F1_WT_mTEC_GFP_ATAC_rep1


title: NSLA_345


title: ATACseq_ESC_snf2l_ko_E_rep2

extract_protocol:
DNA was purified using the MinElute PCR Purification Kit (Qiagen).
PCR amplification with Nextera compatible primers

value: snf2l knock-out


title: IL-2 Fetal M2 [scRNA-seq]

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotech Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw FASTQ data was processed using Cell Ranger v3.0.1
Count matrixes were filtered using Seurat v4.0.1 to remove cell barcodes with less than 700 genes and with more than 15% mitochondrial counts
Seurat v4.0.1 was used to normalize, scale, regress out variation in UMI counts and mitochondrial content, perform dimensionality reduction and generate UMAP projections.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files; containing cell barcodes, genes, and matricies which can be combined to form a Barcodes X Features sparse count matrix for each sample.

source_name: CBMC

extract_protocol:
CD8+ cells were magnetically enriched by positive selection (anti-human CD8 microbeads; Miltenyi Biotech) from rested PBMCs or CBMCs. 2x105 cells were plated per well in round-bottomed 96 well plates. Cells were incubated in RP-10 supplemented with recombinant human IL-2, recombinant human IL-12p70 and recombinant human IL-18 at 10ng/ml for 18-22 hours. Live CD235a- CD4- CD8+ cells were sorted into 0.04% BSA in PBS.
Cells were counted and 3-8k cells per sample were loaded in the Chromium controller for the formation of gel bead-in-emulsions (GEMs) following the manufacturer's instructions (10X Genomics). The single-cell RNA-seq libraries were prepared using Chromium Single Cell 3′ Reagent Kit v3 following the accompanied protocol and were sequenced on Illumina NextSeq500.

value: CD8+ T-cells

value: CBMC

value: Male

value: Fetal (28-29 weeks)

value: IL-2 (control)


title: IL-12/18 Fetal F2 [scRNA-seq]

description: 10x Genomics

value: IL-2/12/18 (bystander activation)


title: ChIPseq_ESC_BPTF_IP_wt_rep1

value: embryonic stem cells


title: NSLA_312


title: ATACseq_ESC_snf2l_ko_E_rep1


title: IL-12/18 Fetal F1[scRNA-seq]

description: 10x Genomics


title: NSLA_311


title: IL-12/18 Fetal M1 [scRNA-seq]

description: 10x Genomics


title: IL-2 Fetal F2 [scRNA-seq]

description: 10x Genomics


title: IL-2 Fetal M1 [scRNA-seq]

description: 10x Genomics


title: NSLA_310


title: IL-12/18 Neonate M2 [scRNA-seq]

description: 10x Genomics

value: Neonate (39-41 weeks)


title: IL-2 Fetal F1 [scRNA-seq]

description: 10x Genomics


title: ATACseq_ESC_wt_E_rep1

value: wt


title: IL-12/18 Neonate F2 [scRNA-seq]

description: 10x Genomics


title: ATACseq_ESC_wt_E_rep2


title: NSLA_300

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: IL-12/18 Neonate F1 [scRNA-seq]

description: 10x Genomics


title: NSLA_350

value: FEMALE


title: NSLA_309


title: IL-2 Neonate M2 [scRNA-seq]

description: 10x Genomics


title: NSLA_2_97

value: MALE


title: IL-2 Neonate M1 [scRNA-seq]

description: 10x Genomics


title: IL-12/18 Adult M2 [scRNA-seq]

description: 10x Genomics

source_name: PBMC

value: PBMC

value: Adult (23-32 years)


title: NSLA_2_8

value: Lung


title: Mouse NK, Mef2c RNP, biol rep 3

city: Los Angeles

first: Joey

middle: Han Tang

last: Li

state: CA

address: 615 Charles E. Young Dr S

institute: UCLA

data_processing:
Bulk RNA-seq fastq files were first checked for quality using FastQC, then trimmed to remove low-quality reads and adaptors using Trimmomatic(version 0.40). The parameters used were SLIDINGWINDOW:4:20 MINLEN:40 LEADING:3 TRAILING:3. Then, reads were aligned to either the reference mouse genome (mm10) or the reference human genome (hg38) with STAR (version 2.7.11). STAR was run with default parameters and the –quantMode geneCounts parameter to generate ReadsPerGene.out.tab files, which are tab-delimited files with the raw number of reads mapped to each gene. The unstranded reads (column 2 of ReadsPerGene.out.tab) were combined into one counts matrix using Excel. Using DESeq2 (version 1.24.0) with default parameters, differential expression analysis was performed, and the counts matrix was normalized. All genes were filtered for significantly differentially expressed genes by p < 0.05. Only genes with counts per million (CPM) > 40 were used for differential expression analysis.
Assembly: hg38, mm10
Supplementary files format and content: Raw counts per gene

source_name: NK cell

extract_protocol:
RNA was isolated from purified NK cells using the Quick-RNA Micro-prep kit (Zymo).
Ribosomal RNA was depleted from samples using the QIAseq FastSelect -rRNA HMR kit (Qiagen). RNA libraries were prepared according to manufacturer instructions using the Stranded Total RNA Prep kit (Illumina, 20040525). Libraries were barcoded using the IDT for Illumina RNA UD Indexes Set A (Illumina, 20040553) and PCR-amplified libraries were cleaned up using Ampure XP beads (Beckman Coulter). Library quality and concentration were assessed by HSD1000 tape on 2200 Tapestation (Agilent) and Qubit 2.0 Fluorometer, and barcoded libraries were pooled to equimolar ratios for sequencing. Sequencing was performed on a NovaSeq 6000 system (Illumina).

value: NK cell

value: MEF2C KO

value: Mef2c RNP


title: Obese CD8 TIL, scRNA-seq

city: St Louis

first: Ryan

middle: M

last: Teague

state: Missouri

address: 1100 S Grand Blvd

department: Molecular Microbiology and Immunology

institute: Saint Louis University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cellranger v 6.0.2
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: B16 F0 transplanted tumor

extract_protocol:
CD8+ TIL were enriched from tumors using CD8+ MicroBeads and separated on LS columns using a QuadroMACS Cell Separator. Enriched TIL were then sorted to at least 99% purity based on CD8 staining using a BD FACSAria III (BD Biosciences).
Single-cell RNA libraries were prepared using the Chromium Single-Cell 3’ Library and Gel Bead Kit. GEM-RT was performed in a T100 96-Well Thermal cycler according to 10X protocol. The GEMs were then broken, and single-stranded cDNA was cleaned up with DynaBeads MyOne Silane Beads. Barcoded, full-length cDNA was amplified using the T100 96-Well Thermal Cycler according to 10X protocol and stored at -20°C. Amplified cDNA product was cleaned up with the SPRIselect Reagent Kit. 3’ gene-expression libraries were constructed using the reagents from the Chromium Single-Cell 3’ Library Construction Kit.

value: B16 F0 transplanted tumor

value: CD8 T Cells

value: Male

value: 16 weeks

tag: phenotype

value: Obese


title: Lean CD8 TIL, scRNA-seq

description: 10x Genomics

value: Lean


title: IL-12/18 Adult F2[scRNA-seq]

description: 10x Genomics

value: CD8+ T-cells

value: Female

value: IL-2/12/18 (bystander activation)


title: NSLA_2_63

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: IL-12/18 Adult F1 [scRNA-seq]

description: 10x Genomics

value: PBMC


title: IL-2 Adult M2 [scRNA-seq]

description: 10x Genomics

value: Adult (23-32 years)

value: IL-2 (control)


title: Mouse NK, Mef2c RNP, biol rep 1

value: NK cell


title: Mouse NK, Mef2c RNP, biol rep 2

value: MEF2C KO


title: IL-2 Adult M1 [scRNA-seq]

description: 10x Genomics


title: NSLA_2_55

value: Lung

value: MALE


title: NSLA_2_5


title: IL-2 Adult F1 [scRNA-seq]

description: 10x Genomics


title: vitamin D bolus, day 1, Individual 26

city: Olsztyn

first: Carsten

last: Carlberg

state: Warmia-Mazury

address: Tuwima 10

department: Food Technology

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description:
After 1 day of vitamin D bolus intake
d1_Ind26

data_processing:
Read alignment using STAR v2.7.2a using defualt parameters
Quantification using FastQC v0.11.9 and Featurecounts v2.0.1 using default parameters
Filtering for protein coding genes and read counts normalization via EdgeR v4.0.14 (TMM-normalized CPM)
Assembly: hg38, Aligned to Ensembl annotation version 111, final annotation (via Biomart) to Ensembl version 111.38
Supplementary files format and content: Excel table of TMM-normalized read counts (CPM; EdgeR pipeline)

source_name: peripheral blood mononuclear cells

growth_protocol: no in vitro culture

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: Before and after intake of 80000 IU of vitamin D3

value: peripheral blood mononuclear cells

tag: disease state

value: Healthy Individuals

value: 80000 IU vitamin D3

tag: time

value: day 1


title: NSLA_2_411

tag: tissue

tag: subject status

value: FEMALE


title: IL-2 Adult F2 [scRNA-seq]

description: 10x Genomics

tag: cell type

value: CD8+ T-cells


title: vitamin D bolus, day 1, Individual 25

description:
After 1 day of vitamin D bolus intake
d1_Ind25


title: Mouse NK, Rosa26, biol rep 2

value: Control

value: Rosa26 RNP


title: Mouse NK, Rosa26, biol rep 3


title: NSLA_2_41

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

tag: Stage

tag: age


title: Mouse NK, Rosa26, biol rep 1

tag: treatment


title: vitamin D bolus, day 1, Individual 24

description:
After 1 day of vitamin D bolus intake
d1_Ind24


title: IL-2 Neonate F1 [scRNA-seq]

description: 10x Genomics

value: CBMC

value: Female

value: Neonate (39-41 weeks)


title: vitamin D bolus, day 1, Individual 22

description:
After 1 day of vitamin D bolus intake
d1_Ind22

value: PBMC


title: vitamin D bolus, day 1, Individual 23

description:
After 1 day of vitamin D bolus intake
d1_Ind23


title: vitamin D bolus, day 1, Individual 21

description:
After 1 day of vitamin D bolus intake
d1_Ind21


title: NSLA_2_407

value: NSCLC

tag: gender


title: IL-12/18 Adult M1[scRNA-seq]

description: 10x Genomics

value: Male

value: Adult (23-32 years)

value: IL-2/12/18 (bystander activation)


title: vitamin D bolus, day 1, Individual 20

description:
After 1 day of vitamin D bolus intake
d1_Ind20

value: peripheral blood mononuclear cells


title: NSLA_2_379

value: Lung


title: AGM E11.5, technical replicate 1, scRNAseq

city: Paris

first: Charles

last: Durand

address: 9, quai saint-Bernard

department: Laboratory of Developmental Biology

country: France

institute: Sorbonne University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
CellRanger software version 4.0.0
Assembly: mm10
Supplementary files format and content: Matrix (.mtx), features (.tsv) and barcodes (.tsv) output files from CellRanger
Supplementary files format and content: Metadata files (.tsv) with UMAP coordinates and cell identities

source_name: Aorta-Gonad-Mesonephros

extract_protocol:
C57BL/6 pregnant mice were used and embryos were collected at E11.5. AGMs were dissected and treated by collagenase treatment to prepare single cell suspension.
Chromium 10X technology v3.1

value: Aorta-Gonad-Mesonephros

tag: development stage


title: NSLA_2_369

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.
We used the TruSeq DNA Library Prep Kit (Illumina, San Diego, CA, USA) for TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) for stranded total RNA-seq library, following the manufacturer’s instructions. For paired-end sequencing was performed using an Illumina NovaSeq 6000 sequencing instrument, the constructed library was sequenced using a HiSeq 4000 sequencing system, resulting in 2× 100 bp sequencing reads.


title: vitamin D bolus, day 1, Individual 16

description:
After 1 day of vitamin D bolus intake
d1_Ind16

value: Healthy Individuals

value: 80000 IU vitamin D3

value: day 1


title: vitamin D bolus, day 1, Individual 14

description:
After 1 day of vitamin D bolus intake
d1_Ind14


title: vitamin D bolus, day 1, Individual 17

description:
After 1 day of vitamin D bolus intake
d1_Ind17


title: NSLA_2_363

value: FEMALE


title: vitamin D bolus, day 1, Individual 13

description:
After 1 day of vitamin D bolus intake
d1_Ind13


title: E14_P16_2iLIF_200 Cells_Day4_Gastruloids_3X Glucose 63.75mM

city: Cambridge

first: Chaitanya

middle: Dnyanehwar

last: Dingare

address: Downing Site

department: Dept of Genetics

country: United Kingdom

institute: University of Cambridge

data_processing:
TrimGalore to trim the index sequences
Hisat2 to obtain BAM/SAM files
Samtools to sort BAM files
Picard Mark Duplicates to remove PCR duplicates
Samtools to sort PCR duplicates removed BAM files
StringTie
Deseq2 to obtain differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Tabular file obtained from StringTie containing Gene counts
Supplementary files format and content: Txt File containing the list of differentitally expressed genes with the FDR lower than 0.05 obtained by running Deseq2. Three comparisons were made No Glucose vs 1X Glucose, 1X Glucose vs 2-DG, and 1X Glucose vs 3X Glucose

extract_protocol:
TRIzol extraction. 2500 ng of total RNA was used to isolate polyA RNA and used for the library preparation.
PolyA mRNA was extracted using NEB's Poly(A) mRNA Magnetic isolation Module and the library was prepared using NEB's NEBNext Ultra II Diractional RNA Library Prep Kit, according to the user's mannual.

tag: cell line

value: Embryonic Stem Cell


title: vitamin D bolus, day 1, Individual 12

description:
After 1 day of vitamin D bolus intake
d1_Ind12


title: NSLA_2_350

data_processing:
STAR mapping (2.9.10) with GeneCount function Assembly: GRCh38 Supplementary files format and content: Genecounts as text formats
Assembly: GRCh38
Supplementary files format and content: txt

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations


title: vitamin D bolus, day 1, Individual 10

description:
After 1 day of vitamin D bolus intake
d1_Ind10


title: E14_P16_2iLIF_200 Cells_Day4_Gastruloids_No Glucose


title: NSLA_2_30

value: MALE


title: E14_P16_2iLIF_200 Cells_Day4_Gastruloids_1X Glucose 21.25mM


title: vitamin D bolus, day 1, Individual 11

description:
After 1 day of vitamin D bolus intake
d1_Ind11


title: vitamin D bolus, day 1, Individual 09

description:
After 1 day of vitamin D bolus intake
d1_Ind09


title: vitamin D bolus, day 1, Individual 08

description:
After 1 day of vitamin D bolus intake
d1_Ind08


title: vitamin D bolus, day 1, Individual 07

description:
After 1 day of vitamin D bolus intake
d1_Ind07


title: NSLA_2_275


title: NSLA_2_28


title: vitamin D bolus, day 1, Individual 06

description:
After 1 day of vitamin D bolus intake
d1_Ind06


title: vitamin D bolus, day 1, Individual 18

description:
After 1 day of vitamin D bolus intake
d1_Ind18


title: AGM E11.5, technical replicate 2, scRNAseq

description: 10x Genomics


title: vitamin D bolus, day 1, Individual 05

description:
After 1 day of vitamin D bolus intake
d1_Ind05


title: E14_P15_2iLIF_200 Cells_Day4_Gastruloids_2-DG 5mM_1X Glucose


title: NSLA_2_273


title: E14_P16_2iLIF_200 Cells_Day4_Gastruloids_2-DG 5mM_1X Glucose


title: vitamin D bolus, day 1, Individual 04

description:
After 1 day of vitamin D bolus intake
d1_Ind04


title: E14_P15_2iLIF_200 Cells_Day4_Gastruloids_1X Glucose 21.25mM


title: vitamin D bolus, day 1, Individual 15

description:
After 1 day of vitamin D bolus intake
d1_Ind15


title: NSLA_2_266


title: vitamin D bolus, day 1, Individual 02

description:
After 1 day of vitamin D bolus intake
d1_Ind02


title: vitamin D bolus, day 1, Individual 01

description:
After 1 day of vitamin D bolus intake
d1_Ind01


title: E14_P15_2iLIF_200 Cells_Day4_Gastruloids_No Glucose


title: Control, day 0, Individual 26

description:
Before vitamin D bolus intake
d0_Ind26

value: control

value: day 0


title: Control, day 0, Individual 25

description:
Before vitamin D bolus intake
d0_Ind25

value: PBMC


title: Control, day 0, Individual 24

description:
Before vitamin D bolus intake
d0_Ind24


title: NSLA_2_263

value: NSCLC


title: Control, day 0, Individual 23

description:
Before vitamin D bolus intake
d0_Ind23


title: E14_P13_2iLIF_200 Cells_Day4_Gastruloids_3X Glucose 63.75mM


title: NSLA_2_252


title: E14_P15_2iLIF_200 Cells_Day4_Gastruloids_3X Glucose 63.75mM


title: E14_P13_2iLIF_200 Cells_Day4_Gastruloids_No Glucose


title: NSLA_2_24


title: ProKR2iCre/R26tdTomato, replicate 2, scRNAseq

city: Albany

first: Paolo

middle: Emanuele

last: Forni

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

description: 10x genomics

data_processing:
Our lab used cellranger count (version4)to perform alignment, filtering, barcode counting, and UMI counting on the fastq files of 6 separate libraries.
We used filtered processed files as input and Seurat 4.3.0 package in R studio to do quality control and downstream cell clustering analysis. Cells with mitochondrial read rate >5% and expressed < 200 genes were  filtered out from our data set.
Assembly: mm10
Supplementary files format and content: tsv and mtx files containing cell barcodes and gene count matrix

source_name: Whole Embryonic Nose

extract_protocol:
5 embryonic noses at embryonic day 14.5 CD1 IGS mice and 1 embryonic nose at embryonic day 14.5 ProKR2iCre/R26tdTomato were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate.
The single cell suspension of the ProKR2iCre/R26tdTomato was sent to SingulOmics to perform FACS, generating sorted and unsorted datasets and high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Single cell library preparation and sequencing were conducted by the Center of Functional Genomics (CFG) (https://www.albany.edu/genomics/ngs.html, Albany, NY) and Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cell suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 5 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole Embryonic Nose

tag: strain

value: Embryonic day 14.5


title: Control, day 0, Individual 16

description:
Before vitamin D bolus intake
d0_Ind16


title: Control, day 0, Individual 20

description:
Before vitamin D bolus intake
d0_Ind20


title: Control, day 0, Individual 17

description:
Before vitamin D bolus intake
d0_Ind17


title: NSLA_2_221


title: Control, day 0, Individual 18

description:
Before vitamin D bolus intake
d0_Ind18


title: E14_P13_2iLIF_200 Cells_Day4_Gastruloids_1X Glucose 21.25mM


title: vitamin D bolus, day 1, Individual 03

description:
After 1 day of vitamin D bolus intake
d1_Ind03


title: NSLA_2_220


title: Control, day 0, Individual 14

description:
Before vitamin D bolus intake
d0_Ind14


title: NSLA_2_265


title: ProKR2iCre/R26tdTomato, replicate 1, scRNAseq

description: 10x genomics


title: Control, day 0, Individual 15

description:
Before vitamin D bolus intake
d0_Ind15


title: NSLA_2_19


title: Control, day 0, Individual 12

description:
Before vitamin D bolus intake
d0_Ind12


title: RNAseq_ESC_acf1_ko_E_2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.
Assembly: mm10
Supplementary files format and content: csv, count table

extract_protocol:
RNA was extracted with Qiagen Rneasy Mini Kit following manufacture's instruction.. Potential contaminating genomic DNA was removed using Invitrogen DNA-free removal kit, following manufacture's instructions.
Sequencing libraries were prepared from 100ng of purified total RNA using TruSeq stranded mRNA Library Prep (Illumina).

value: embryonic stem cells

tag: genotype

value: acf1 knock-out


title: E14_P13_2iLIF_200 Cells_Day4_Gastruloids_2-DG 5mM_1X Glucose


title: Control, day 0, Individual 13

description:
Before vitamin D bolus intake
d0_Ind13

value: peripheral blood mononuclear cells


title: NSLA_2_184

value: Lung


title: Control, day 0, Individual 11

description:
Before vitamin D bolus intake
d0_Ind11

value: Healthy Individuals


title: Control, day 0, Individual 09

description:
Before vitamin D bolus intake
d0_Ind09


title: Control, day 0, Individual 21

description:
Before vitamin D bolus intake
d0_Ind21


title: Control, day 0, Individual 10

description:
Before vitamin D bolus intake
d0_Ind10


title: NSLA_2_171


title: RNAseq_ESC_acf1_ko_E_1


title: Control, day 0, Individual 08

description:
Before vitamin D bolus intake
d0_Ind08


title: NSLA_2_152


title: Control, day 0, Individual 07

description:
Before vitamin D bolus intake
d0_Ind07


title: RNAseq_ESC_wt_E_1

value: wild-type


title: Control, day 0, Individual 06

description:
Before vitamin D bolus intake
d0_Ind06


title: NSLA_2_136


title: RNAseq_ESC_cecr_ko_D_3

value: cecr knock-out


title: RNAseq_ESC_cecr_ko_D_2


title: Control, day 0, Individual 05

description:
Before vitamin D bolus intake
d0_Ind05


title: Control, day 0, Individual 03

description:
Before vitamin D bolus intake
d0_Ind03


title: NSLA_2_121


title: Control, day 0, Individual 01

description:
Before vitamin D bolus intake
d0_Ind01


title: Control, day 0, Individual 02

description:
Before vitamin D bolus intake
d0_Ind02


title: NSLA_2_118


title: Control, day 0, Individual 04

description:
Before vitamin D bolus intake
d0_Ind04


title: RNAseq_ESC_cecr_ko_D_1


title: NSLA_2_116


title: RNAseq_ESC_wt_D_3


title: RNAseq_ESC_wt_E_2


title: NSLA_291

value: FEMALE


title: RNAseq_ESC_wt_D_2


title: NSLA_271


title: RNAseq_ESC_wt_D_1


title: Don3 OM300+Anti-TLR4 2hr

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine (IRB)

data_processing:
We used FastQC v0.11.9 to assess the quality of the reads. Adapters sequences were removed using Trimmomatic v0.39.
Reads were subsequently mapped to the human genome using HISAT2 v2.1.0.
We then usedHTSeq-count v2.0.2 to generate the table of counts containing the number of reads mapping to each feature in each sequencing sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Blood

growth_protocol: Mo-DCs were differentiated in vitro from human CD14+ monocytes of 3 healthy donors using GM-CSF and IL-4 and harvested on d5.

extract_protocol:
Total RNA was extracted from sorted cells with a RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions. The quantity and quality of the isolated RNA was determined with a Qubit (1.0) Fluorometer (Life Technologies) and a 4200 TapeStation System (Agilent).
NEBNext Ultra DirectionalRNA Library Prep Kit for Illumina (New EnglandBioLabsInc.) was employed with theNEBNextMultiplex Oligos for Illumina (New EnglandBioLabsInc.) andNEBNext®Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The sequencing of the pre-pools was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100cycles; Illumina).

treatment_protocol: Mo-DCs treated with the bacterial lysate OM-85 at the indicated concentrations (ug/ml) for the indicated timepoints. In case of samples 49-76 Mo-DCs were pre-treated with isotype control antibody or blocking antibodies agaisnt TLR2 or TLR4 or both for 90 min followed by stimulation with 300 ug/ml OM-85, 0.1 ng/ml LPS or 10ng/ml Pam3CSK4 for 2hr.

value: Blood

tag: subject

value: Mono-derived DC

value: WT

value: OM-85 300ug/ml 2hr+Anti-TLR4 Ab


title: Don3 OM300+ISO 2hr

value: OM-85 300ug/ml 2hr+Isotype Control Ab


title: Don3 Pam3+ISO 2hr

value: Pam3CSK4 10ng/ml+Isotype Control Ab


title: Don3 LPS+ISO 2hr

value: LPS 1ng/ml+Isotype Control Ab


title: Don3 OM300+Anti-TLR2/4 2hr

value: OM-85 300ug/ml 2hr+Anti-TLR2/4 Ab


title: Don3 UT+ISO 2hr

value: UT+Isotype Control Ab


title: NSLA_259

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: Control, day 0, Individual 22

description:
Before vitamin D bolus intake
d0_Ind22

value: peripheral blood mononuclear cells

value: PBMC

value: control

value: day 0


title: Don2 OM300+Anti-TLR2/4 2hr


title: NSLA_257

value: Lung


title: Don2 OM300+Anti-TLR4 2hr


title: NSLA_251

value: FEMALE


title: Don2 OM300+ISO 2hr

value: Blood


title: Don2 Pam3+ISO 2hr

value: Mono-derived DC


title: Don2 LPS+ISO 2hr

value: WT


title: Don2 OM300+Anti-TLR2 2hr

value: OM-85 300ug/ml 2hr+Anti-TLR2 Ab


title: NSLA_239


title: Don1 OM300+Anti-TLR2/4 2hr


title: Don2 UT+ISO 2hr


title: Mouse_Lung_fixed_cryo

city: Barcelona

first: Laura

last: Jiménez-Gracia

address: c/ Baldiri Reixac, 4  Barcelona Science Park - Tower I

country: Spain

institute: Centre Nacional d'Anàlisi Genòmic (CNAG)

description:
uyzd7xqc_jkya4jyl
10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10; GRCh38

extract_protocol: The Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-  1000268, 10X Genomics) were used to prepare cDNA sequencing libraries, following the  manufacturer's instructions. Briefly, after GEM-RT clean up, cDNA was amplified for 11  cycles and then subjected to quality control and quantification using an Agilent Bioanalyzer  High Sensitivity chip (Agilent Technologies). The Dual Index Kit TT Set A (PN-1000215, 10X  Genomics) was used for indexing cDNA libraries by PCR. The size distribution and  concentration of 3' cDNA libraries were verified again on an Agilent Bioanalyzer High  Sensitivity chip (Agilent Technologies). The cDNA libraries were sequenced on an Illumina  NovaSeq 6000 using the following sequencing conditions: 28 bp (Read 1) + 8 bp (i7 index) +  0 bp (i5 index) + 89 bp (Read 2) to generate approximately 40,000 read pairs per cell.

tag: type

value: fixed cryo


title: Don3 OM300+Anti-TLR2 2hr


title: NSLA_235


title: Mouse_Lung_fixed_24h

description:
wa4ylezj_f7kjs3op
10x Genomics

value: fixed 24h


title: Mouse_Lung_cryo

description:
btvimge6_fuk14b5o
10x Genomics

value: cryo


title: NSLA_216


title: Don1 Pam3+ISO 2hr

value: Pam3CSK4 10ng/ml+Isotype Control Ab


title: Don1 OM300+Anti-TLR2 2hr


title: Don1 LPS+ISO 2hr

value: LPS 1ng/ml+Isotype Control Ab


title: Mouse_Lung_fresh

description:
pfgvxfe6_ftr5tlpm
10x Genomics

value: fresh


title: Don1 UT+ISO 2hr

value: UT+Isotype Control Ab


title: Don1 OM300+ISO 2hr

value: OM-85 300ug/ml 2hr+Isotype Control Ab


title: NSLA_20

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: Don3 OM900 8hr

value: OM-85 900ug/ml 8hr


title: NSLA_187

value: Lung


title: Don3 OM300 8hr

value: OM-85 300ug/ml 8hr


title: Mouse_Colon_fresh

description:
xoxslu7q_8nia4zwr
10x Genomics

source_name: Colon

value: Colon


title: Don3 OM100 8hr

value: Blood

value: Mono-derived DC

value: OM-85 100ug/ml 8hr


title: Don3 UT 8hr

value: WT

value: UT 8hr


title: NSLA_181

value: FEMALE


title: Don1 OM300+Anti-TLR4 2hr

value: OM-85 300ug/ml 2hr+Anti-TLR4 Ab


title: Don3 OM300 2hr

value: OM-85 300ug/ml 2hr


title: Don3 OM900 2hr

value: OM-85 900ug/ml 2hr


title: NSLA_179


title: Don3 OM100 2hr

value: OM-85 100ug/ml 2hr


title: Healthy control Male 9-11 weeks replicate 4 [Healthy-CTRL-Male-13]

city: Marseille

first: Bianca

middle: Hermine

last: Habermann

address: Avenue de Luminy 163

institute: IBDM UMR7288

data_processing:
Quality control was performed on the fastq files using FastQC (v0.11.9). To map the sequenced reads to the mouse reference genome (GRCm39 from NCBI), we used STAR (v2.7.3a). From these mapped reads, gene counts were then quantified using featureCounts (v2.0.1). Starting from the raw gene counts, normalization and differential expression analysis was then performed using DESeq2 (v 1.22.2).
Assembly: GRCm39
Supplementary files format and content: csv file for normalized read counts
Supplementary files format and content: csv file for differential expression analysis (DESeq2)

source_name: gastrocnemius skeletal muscle

extract_protocol:
Total RNA was isolated from ≈25mg of the gastrocnemius skeletal muscle using both TRIzol (Invitrogen) and the Qiagen total RNA isolation kit (Qiagen, ref 74004) to avoid protein and extracellular matrix accumulation in the columns. Briefly, muscle piece was lysed in 600 µL RLT Buffer (from Qiagen kit) with 1% β-Mercaptoethanol using beads tube from Precellys lysing kit for hard tissue (P000917-LYSK0-A; 3x Cycle 1500 rpm, 15 s of mix, 10 s of rest) and directly centrifuged 3 min at 10,000g at RT. Supernatant was transferred in 400µL of TRIzol and incubated for 5 min at RT followed by addition of 150µL of chloroforme. Tubes were carefully mixed and incubated 3 min at RT before centrifugation (12,000g, 5min, 4°C). The transparent upper phase containing RNAs was transferred in a tube containing 500 µL of 70% ethanol, mixed and transferred inside Qiagen RNA isolation kit columns according to manufacturer’s instructions followed until the end of extraction. Samples were treated with RNase-free DNase on Qiagen spin-columns to remove DNA contamination. RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). The average RIN (RNA integrity number) values for all samples was comprised between 9.3 and 10, ensuring a high quality of isolated RNAs.
The preparation of mRNA libraries was realized following manufacturer’s recommendations (kapa mRNA HyperPrep from ROCHE). Final samples pooled library prep were sequenced on ILLUMINA Novaseq 6000 with S1-200cycles cartridge (2x1600Millions of 100 bases reads), corresponding to 2x30Millions of reads per sample after demultiplexing.

treatment_protocol: one gastrocnemius muscle was fast frozen in isopentane cooled on dry ice, and stored at −80° C for RNA and protein analysis.

value: gastrocnemius skeletal muscle

value: LSL-KrasG12D;Ink4a/Arffl/fl (KI)


title: Healthy control Male 9-11 weeks replicate 2 [Healthy-CTRL-Male-9]


title: NSLA_172

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: Don3 UT 2hr

value: UT 2hr


title: Healthy control Male 9-11 weeks replicate 3 [Healthy-CTRL-Male-12]


title: Don2 OM300 8hr

value: OM-85 300ug/ml 8hr


title: NSLA_168

value: Lung


title: Don2 OM900 8hr

value: Blood

value: OM-85 900ug/ml 8hr


title: Healthy control Male 9-11 weeks replicate 1 [Healthy-CTRL-Male-8]


title: Don2 OM100 8hr

value: Mono-derived DC

value: OM-85 100ug/ml 8hr


title: Cancer KIC Male 9-11 weeks replicate 4 [Cancer-KIC-Male-10]


title: Mouse_Colon_fixed_24h

description:
bmgc51ex_jits5na1
10x Genomics

value: Colon

value: fixed 24h


title: NSLA_198

value: FEMALE


title: NSLA_14


title: Don2 OM900 2hr

value: WT


title: Cancer KIC Male 9-11 weeks replicate 3 [Cancer-KIC-Male-9]


title: NSLA_139


title: Don2 OM100 2hr


title: Cancer KIC Male 9-11 weeks replicate 2 [Cancer-KIC-Male-8]


title: NSLA_138


title: Don2 UT 2hr


title: E3_derived

city: Madrid

first: Rafael

last: Torres

state: Madrid

address: Darwin 3

department: Bioinformatics for Genomics and Proteomics (BioinfoGP)

institute: CNB

data_processing:
The quality of the sequences obtained was analyzed using the FastQC program.
Read alignment and quantification was performed using Rockhopper (PMID: 23716638).
Assembly: Assembly genome ASM676v1 (NCBI Reference Sequence: NC_002516.2).
Supplementary files format and content: Pseudorevertants_expression.txt is a tab-separated file containing the raw counts corresponding all (11) samples analized. Gene identifiers columns are: Name=gene name; Synonym=Uniprot Primary Accession; Product=Product description in NCBI Protein.

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cells

growth_protocol: Samples were obtained by centrifugation (7000 rpm, 20 min, 4 °C) of a bacterial culture in exponential phase in LB medium (OD600 ≈ 0.6). The sediment was kept at ‐80 °C until processing, for a maximum of 1 month.

extract_protocol:
Lysozyme was added to this pellet to a final concentration of 1 mg/ml. It was incubated for 10 min at room temperature with intermittent vortexing. Sonication was performed for 3 intermittent cycles of 20 s (0.4 power) followed by incubation periods at 4 °C. RNA extraction continued with the commercial RNA easy minikit (QIAGEN) system. DNA was removed using the RNase-Free DNAse Set (QIAGEN), and possible DNA debris with the Turbo DNA-free system (AMBION). DNA contamination was ruled out by PCR with the rplU gene primers. Ribosomal RNA was removed with the Ribo‐Zero Magnetic Kit Bacteria system (Epicentre).
The library was prepared using 3.5 μg of treated RNA, with the TruSeq RNA sample preparation kit v2 system (Illumina).
The RNA-seq experiment was performed at the Antonia Martín Gallardo Genomics Unit, Parque Científico de Madrid, with the Genome Analyzer IIx (Illumina) in a single reading format (1x75 nt).

value: bacterial cells

tag: background strain

value: derived from delta_crcZ; FAA resistant


title: E5_derived


title: Cancer KIC Male 9-11 weeks replicate 1 [Cancer-KIC-Male-7]

value: gastrocnemius skeletal muscle


title: E2_derived


title: NSLA_136

city: daejeon

first: Seung-Jin

address: gwahakro

institute: KRIBB

source_name: Lung


title: Don1 OM300 8hr


title: NSLA_1013


title: Don1 OM900 8hr


title: NSLA_1012


title: E1_derived


title: hippocampus, Saline, rep6

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FASTQ-file generation and demultiplexing using bcl2fastq 2.20.0
Add UMIs to header in FASTQ-files using bash script
Align to genome and determine transcript and gene counts with the nfcore-rnaseq pipeline v. 3.8.1 using the STAR->Salmon workflow.
Assembly: GRCm38
Supplementary files format and content: Tab-seperated file containing the raw gene counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample
Supplementary files format and content: Tab-seperated file containing the raw transcript counts for each sample. Rows specify genes by ENSEMBL_ID, and columns specify the sample

source_name: hippocampus

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, #74106) according to the manufacturer’s protocol.
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter), DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality-controlled using a Fragment Analyzer instrument (Agilent Technologies) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 2.7 billion reads were generated.

treatment_protocol: DIO mice (average body weight 53g, double-housed) were injected with 56 mg/kg mPD5 (n=8), 25 mg/kg UCCB01-147 (n=8) or isotonic saline (n=6) daily, for 5 days. On experimental days 1 to 4, injections were performed 2 hours before the onset of the dark phase. Body weight and food intake were measured daily. On the morning of the 5th experimental day, mice were injected and sacrificed 2 hours later. Whole hypothalamus was flash frozen on dry ice in preparation for RNA isolation.

value: hippocampus

value: Saline


title: Don1 OM100 8hr


title: Don2 UT 8hr

value: UT 8hr


title: hippocampus, PSD-95i, rep8


title: R5_derived

value: derived from delta_crcZ; FAA susceptible


title: Don1 UT 8hr


title: NSLA_1011

last: Park

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: NSCLC


title: Don2 OM300 2hr

value: Blood

value: OM-85 300ug/ml 2hr


title: hippocampus, PSD-95i, rep7


title: NSLA_1010

value: Lung


title: Don1 OM900 2hr

value: Mono-derived DC

value: OM-85 900ug/ml 2hr


title: hippocampus, PICK1i, rep7


title: Don1 OM300 2hr


title: hippocampus, PICK1i, rep8


title: hippocampus, Saline, rep7


title: delta-crcZ

description: delta-crcZ


title: NSLA_101


title: R4_derived


title: NSLA_1009


title: delta-crc

description: delta-crc


title: hippocampus, PSD-95i, rep5


title: WT

description: WT


title: NSLA_1008


title: Don1 OM100 2hr

value: OM-85 100ug/ml 2hr


title: NSLA_1007

value: FEMALE


title: hippocampus, PSD-95i, rep4


title: THP1 wt, rep4

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

data_processing:
The alignment was conducted with STAR 2.7.0c against the human reference genome hg38 with default parameters.
The resulting bam file was sorted and reads with ambiguous mapping were removed with SAMtools 1.9.
Read counts per gene were counted with the R package bamsignals 3.8.
DESeq2 was used to identify differentially expressed genes per condition.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: AML

growth_protocol: THP1 monocytic cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 µg of total RNA per sample was used as starting material.
The NEBNext® Ultra™ II RNA Library Prep Kit (Cat. No. E7770), the NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat. No. E7490) and the NEBNext® Multiplex Oligos for Illumina® (Cat. No. E7335 and E7500S) were used for the library preparation of RNA samples according to the manufacturer’s instructions.
A deep sequencing of the RNA libraries (30x10E6 reads per sample) was carried out on the Illumina NextSeq 500

treatment_protocol: Where indicated cells were treated with 100nM 4-OHT for PHF8AA or PHF8DD induction.

value: AML

value: monocytic MLL-AF9

value: wt


title: R2_derived

value: bacterial cells


title: hippocampus, PICK1i, rep6

value: hippocampus


title: THP1 wt, rep2


title: THP1 wt, rep3


title: hippocampus, PSD-95i, rep3


title: HIF1α-mutant 24h hypoxia rep 3

city: London

first: Dimitrios

last: Anastasiou

address: 1 Midland Road

department: Cancer Metabolism Laboratory

institute: The Francis Crick Institute

data_processing:
Transcript reads were aligned to the Ensembl GRCh37 genome using Tophat2 v2.1.1 (with option --no-coverage-search).
Gene expression was normalised using DeSeq2 v1.16.1 with default settings.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: tab delimited, contains normalised read counts

growth_protocol: MCF7 cells were were cultured in high-glucose DMEM (Gibco, Cat# 11960-085) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine and 100 U/mL penicillin/streptomycin in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
Cells were washed 3x with PBS and harvested in 1 ml TRIzol Reagent (Thermo Fisher Scientific). Chloroform (0.2 ml, Acros Organics) was added to lysates and after shaking (5s) samples were centrifuged for 18 min at 10,000 x g. The  aqueous phase was mixed with an equal volume of 100% ethanol (500 μl) and RNA was purified using the RNeasy Kit (Qiagen), according to the manufacturer's instructions.
Libraries were prepared using the KAPA Hyper Prep kit (Roche) according to the manufacturer's instructions.

treatment_protocol: Hypoxia treatments for 3 or 24 hours were performed in a Baker Ruskinn InVivo2 400 hypoxic workstation at 1% O2, 5% CO2, 37°C and 70% humidity.

value: breast adenocarcinoma

tag: genotype/variation

value: hypoxia (1% oxygen, 24 hours)


title: HIF1α-mutant 24h hypoxia rep 2


title: NSLA_1006


title: NSLA_1004


title: hippocampus, PICK1i, rep5


title: R1_derived

value: derived from delta_crcZ; FAA susceptible


title: hippocampus, PSD-95i, rep6


title: THP1 wt, rep1


title: HIF1α-mutant 24h hypoxia rep 1


title: NSLA_1003

value: Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations

value: MALE


title: THP1 PHF8, rep4


title: hippocampus, PSD-95i, rep2


title: THP1 PHF8, rep3


title: NSLA_1002

value: NSCLC


title: Don1 UT 2hr

value: Blood

value: WT

value: UT 2hr


title: wt 24h hypoxia rep 3

value: wild type


title: wt 24h hypoxia rep 2


title: NSLA_1001

value: Lung


title: hippocampus, PSD-95i, rep1


title: hippocampus, Saline, rep5

value: Saline


title: THP1 PHF8, rep2

value: AML


title: wt 24h hypoxia rep 1


title: THP1 PHF8, rep1

value: monocytic MLL-AF9


title: HIF1α-mutant 3h hypoxia rep 3

value: hypoxia (1% oxygen, 3 hours)


title: hippocampus, Saline, rep4


title: NSLA_1005

value: FEMALE


title: Brain Organoid Lineagetracing Day 42 Replicate 2

city: Vienna

first: Simon

middle: Emanuel

last: Haendeler

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

data_processing:
Library strategy: Lineage tracing with genomic barcoding
Demultiplexing by extraction of sample barcode in b2 tag concatenated with bc tag and allowing for one missmatch when comparing to known sample barcodes
LID error correction by UMI-tools algorithm
Removal of LIDs that occure in multiple samples with threshold 0.95
Filtering of LIDs with low read count
The sample.csv includes sample barcodes used for demultiplexing and the read threshold that is applied during analysis.
Assembly: not applicable
Supplementary files format and content: lineage size of every lineage in sample as csv

source_name: Brain Organoid

growth_protocol: Two retroviral libraries based on pRSF retrovirus expressing TagBFP were used for lineage tracing. hESC cells infected. Single stem cell suspensions were prepared, sorted for TagBFP and plated in Essential 8 media supplemented with RevitaCell to recover for 1-2 days before the organoid protocol was initiated.

extract_protocol:
Genomic DNA was extracted by phenol/chloroform extraction.
After 12 freeze/thaw cycles only the viral barcode inserts were amplified by using lineage tracing genomic DNA primers, which also introduced sequencing adaptors

value: Brain Organoid

value: hESC

tag: timepoint

value: Day 42


title: Brain Organoid Lineagetracing Day 42 Replicate 1


title: THP1 F279S, rep4


title: THP1 F279S, rep3


title: hippocampus, Saline, rep2

value: hippocampus


title: Brain Organoid Lineagetracing Day 11 Replicate 2

value: Day 11


title: THP1 F279S, rep2


title: wt 3h hypoxia rep 3

value: breast adenocarcinoma


title: Brain Organoid Lineagetracing Day 11 Replicate 3


title: Brain Organoid Lineagetracing Day 11 Replicate 1


title: THP1 F279S, rep1


title: Brain Organoid Lineagetracing Day 6 Replicate 3

value: Day 6


title: wt 3h hypoxia rep 2


title: hippocampus, Saline, rep1


title: THP1+ERPHF8, rep2, d3


title: wt 3h hypoxia rep 1


title: Brain Organoid Lineagetracing Day 6 Replicate 2


title: hippocampus, PICK1i, rep2


title: HIF1α-mutant normoxia rep 3

value: normoxia


title: THP1+ERPHF8, rep1, d3


title: Brain Organoid Lineagetracing Day 6 Replicate 1


title: HIF1α-mutant 3h hypoxia rep 2


title: hippocampus, Saline, rep3


title: THP1+ERDD, rep2, d3


title: HIF1α-mutant normoxia rep 2


title: HIF1α-mutant 3h hypoxia rep 1


title: hippocampus, PICK1i, rep1


title: THP1+ERDD, rep1, d3


title: Brain Organoid Lineagetracing Day 1 Replicate 1

value: Day 1


title: hippocampus, PICK1i, rep4


title: Brain Organoid Lineagetracing Day 1 Replicate 3


title: THP1+ERAA, rep2, d3


title: HIF1α-mutant normoxia rep 1


title: PFC, Saline, rep7

source_name: PFC

value: PFC


title: wt normoxia rep 3

value: wild type


title: PFC, Saline, rep8


title: THP1+ERAA, rep1, d3


title: hippocampus, PICK1i, rep3


title: PFC, PSD-95i, rep8


title: DD PHF8WT replicate 2

data_processing:
FastQC 0.11.9 was used for standard quality controls of the ChIP-seq fastq data.
Raw ChIP-seq reads were aligned to the human reference genome hg38 with BWA 0.7.17, and subsequently sorted with SAMtools 1.9.
Ambiguous and duplicate reads were removed with the SAMtools program suite (v1.9).
Peaks were identified for both separate and merged replicates with MACS2 and default parameters; a q-value cutoff <= 0.05 was used.
Assembly: hg38
Supplementary files format and content: MACS2 narrowPeaks for single samples and merged replicates per condition (except for IgG sample, which was used as control in all peak calculations)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a focused-ultrasonicator S2 Covaris.
One ng per sample of fragmented and purified DNA as starting material was used. The size of the DNA fragments was checked on the Agilent TapeStation and an average of fragments between 300-400 base pairs was obtained.

treatment_protocol: Cells were treated with 100nM 4-OHT for PHF8AA or PHF8DD induction.


title: wt normoxia rep 1


title: PFC, PSD-95i, rep7


title: Mut2_rep1

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

data_processing:
Base calls and demultiplexing were performed with illumina's bcl2fastq software
fastq files were aligned to gencode hg38 transcriptome with STAR (v.2.7.8a) using the Partek flow platform
Alligned reads were quantified to the annotation model (Partek E/M) and normalized to counts per million
Differentially expressed genes (³4-fold and 0.25% false discovery rate) were identified by gene set specific analysis in Partek flow
Assembly: human NCBI genome build 38
Supplementary files format and content: Partek_Brain_organoids_D65_C_and_MCT8KO_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt
Supplementary files format and content: txt file  contaiing the gene counts for each gene and samples

source_name: iPSCs-derived cerebral organoid

growth_protocol: Cerebral organoids derived from iPSCs were grown for 65 days

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were pair-end sequencedwith NovaSeq4 Illumina

treatment_protocol: From day 50 to 65 were treated with 60nM T3

value: iPSCs-derived cerebral organoid

value: iPSCs

value: 15 days 60nM T3 (from D50 to D65)


title: wt normoxia rep 2


title: WT_rep3

value: Wildtype


title: PFC, PICK1i, rep8


title: R1-M-opt48-N-H3K9me3

city: STANFORD

first: Katja

last: Pekrun

address: 269 Campus Drive

department: Pediatrics & Genetics

institute: Stanford School of Medicine

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the mm10 build of the mouse genome, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: mm10
Supplementary files format and content: Bedgraph

source_name: liver

extract_protocol:
Mice were sacrificed 10 weeks after rAAV injection and liver tissue was pulverized and flash-frozen in aliquots. Liver tissue (~100 mg) was homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 4 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. Nuclei were quantitated after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 1e5 nuclei per target protein were used for Cut&Tag.
Nuclei were mixed with activated Concanavalin A beads. After successive incubations with primary antibody (overnight) and secondary antibody (for 30 min) in antibody and Digitonin150 buffer respectively, the beads were washed with Digitonin150 buffer and resuspended in Digitonin300 buffer with 2.5uL of pA(G)-Tn5 for 1 hr and washed with the same buffer. Incubations were performed at room temperature in low-retention PCR strip tubes (Epicypher). Tagmentation was performed for 1 hr at 37C in Tagmentation buffer that provides MgCl2. Beads were washed with TAPS buffer and DNA material was released by adding SDS Release Buffer and incubating at 58C for 1hr. Quenching of SDS was performed by adding SDS Quench buffer and PCR was performed directly on this material. Universal P5 and indexed P7 primer solutions were used (see Supplemental Table 3 for sequences), and 17 cycles of PCR were performed. Clean-up was performed with AMPure beads, eluted in 15uL 0.1x TE buffer. Qubit and Bioanalyzer were used to verify library qualities before pooling samples for sequencing. The barcoded libraries were mixed to achieve equimolar representation aiming for a 10nM final concentration.
Cut & Tag. Sequencing of the same library was performed twice (R1, R2), once with Illumina HiSeq 4000 and once with Illumina NovaSeq SP100, 150 cycles total per lane, 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Mice were intravenously injected with rAAV packaged using the KP1 capsid. The rAAV vector expressed CpG depleted, codon-optimized huFIX under control of a liver-specific promoter.

value: liver


title: DD PHF8WT replicate 1

value: AML

value: monocytic MLL-AF9


title: WT_rep2


title: AA PHF8WT IgG


title: WT_rep1


title: PFC, PICK1i, rep7


title: R1-M-opt48-N-H3K4me3


title: Mut1_rep2


title: Mut2_rep2


title: R1-M-opt48-N-H3K27me3


title: PFC, PSD-95i, rep6


title: Mut1_rep1


title: AA PHF8WT replicate 1


title: RNAseq_ESC_snf2l_ko_F_2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Assembly: mm10
Supplementary files format and content: Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.

source_name: embryonic stem cells

value: embryonic stem cells

value: snf2l knock-out


title: R1-M-opt46-N-H3K9me3


title: G3M,SP6KO,P300_SI_rep2

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

country: China

institute: Inner Mongolia University

data_processing:
Adapters were removed and low-quality bases were trimmed using cutadapt (version 4.3) with the following parameters: -q 20 –O 10 -m 30 --max-n 0.1 --trim-n.
Clean paired-end reads were then mapped to human reference genome hg19 using Bowtie2 (version 2.2.5). Samtools (version 1.13) was used to sort the mapped reads, and reads with MAPQ less than 30 were discarded.
PCR duplicates were removed by Picard (version 2.7). Finally, peak calling was performed by MACS2 (version 2.2.7.1) with the parameter “--broad --nomodel --nolambda –keep-dup all” except for P300-ChIP. For P300-ChIP, peak calling was performed by MACS2 with the following parameters: --nomodel --nolambda –keep-dup all --call-summits -B --SPMR -p 0.001.
The peaks were annotated by homer (version 4.11) with default parameters. Homer annotated intergenic regions with H3K27ac modifications were defined as enhancers. GO enrichment analysis was performed by using rGREAT (version 2.0.2) with default parameters.
Assembly: Human reference genome hg19
Supplementary files format and content: bigWig, broadPeak
Supplementary files format and content: Fragments data contains fragment position

source_name: cell line

extract_protocol:
Cells were resuspended with 80 µl Antibody Buffer (mix 4 µl 0.5 M EDTA with 1 ml 0.01% Digitonin-Wash Buffer (Dig-Wash Buffer) supplemented with cocktail, 10 mM sodium butyrate and 0.05% Triton X-100) containing 0.4 µg primary antibody. The mixture was incubated at 4°C for 4 h in a rotator with 30 rpm. Cells were then washed twice with 180 µL Dig-Wash Buffer. The secondary antibody (1:500 use) was incubated in the same buffer and condition except for the duration of 10 min. After washing with Dig-Wash Buffer twice, cells were suspended with 80 µl Dig-Wash Buffer (with 0.05% Triton-X, cocktail, and 10 mM sodium butyrate) containing 0.83 µM PAT-MEA/B at 4°C for 1 h. The free PAT-MEA/B were then dislodged with 180 µl Dig-Wash Buffer containing 0.05% Triton X-100 three times at 5 min each time. The reaction was activated by suspending the cells with 10 µl Reaction Buffer (10 mM TAPS-NaOH pH 8.3, 5 mM MgCl2, 10% DMF, 300 mM NaCl, 0.05% Triton-X, 0.01% Digtonin and supplemented with cocktail, 10 mM sodium butyrate), followed by gently flicking and incubating at 37°C for 1 h in the Eppendorf ThermoMixer with 300 rpm. The reaction was gently mixed once after 30 min incubation and stopped by the addition of 10 µl 40 mM EDTA followed by further incubation at 4°C for 10 min. Samples were washed with 0.1% BSA/PBS and finally resuspended in 5 µl Lysis Buffer and lysed at 55°C for 3 h in a PCR cycler. 1.8% Triton X-100 with 5 mM PMSF was added to the cell lysate and incubated at RT for 10 min to quench the proteinase K followed by incubation at 55°C for 5 min to quench SDS in the reaction. For H3K27ac and P300 samples, Spike-In DNA (0.1 mg/ml Proteinase K, 10 mM Tris-HCl PPH 8.5 and 0.05% SDS, 20 pg Tn5 tagmenated Drosophila DNA) was added in the Lysis Buffer.
PCR amplification was performed by the addition of 1μl of 10 μM i5 index primer (5’-AATGATACGGCGACCACCGAGATCTACAC[8 bp index]TCGTCGGCAGCGTC-3’), 1 μl of 10 μM i7 index primer (5’-CAAGCAGAAGACGGCATACGAGAT[8 bp index] GTCTCGTGGGCTCGG-3’), 30 μL of 2ⅹKAPA master mix and 23 μl of 1 mM MgCl2 to the cell lysate. The reaction was set up by incubation at 72 °C for 5 min, 98°C for 45 s, 16-18 cycles of amplification (98°C for 15 s, 63°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. After PCR, for histone-ChIP, DNA fragments were size-selected: first 0.4X AMPure beads to remove > 1 kb fragments, and second 0.6X AMPure bead to retain 200-1000 bp fragments; for TF-ChIP, > 1 kb fragments were first removed by using 0.4X AMPure beads, then library was purification by Zymo DNA Clean and Concentrator-5 Kit. All libraries were sequenced with paired-end 150-bp reads on NovaSeq 6000 platform (Illumina).

value: cell line

value: trophoblast cell

value: knock out

tag: chip antibody

value: TSCM


title: AA PHF8WT replicate 2

tag: tissue


title: R1-M-opt48-N-H3K27ac


title: PFC, PSD-95i, rep5


title: PFC, PSD-95i, rep3


title: PFC, PSD-95i, rep4


title: RNAseq_ESC_snf2l_ko_F_1


title: PFC, PICK1i, rep6


title: RNAseq_ESC_wt_F_2

value: wild-type


title: R1-M-opt46-N-H3K27me3


title: R1-M-opt46-N-H3K4me3


title: G3M,CON,P300_SI_rep2

value: knock in


title: G3M,SP6KO,P300_SI_rep1


title: RNAseq_ESC_wt_F_1


title: R1-M-opt46-N-H3K27ac


title: PFC, PICK1i, rep5

value: PFC


title: G3M,CON,P300_SI_rep1


title: PFC, PSD-95i, rep2


title: G3M,SP6KO,H3K27ac_SI_rep2


title: PFC, PSD-95i, rep1


title: G3M,SP6KO,H3K27ac_SI_rep1


title: PFC, Saline, rep6

value: Saline


title: ChIPseq_ESC_Wapl_IP_wt_rep1

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig

extract_protocol:
DNA was purified using AMPure XP beads
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) with 12 PCR amplification cycles for Ips and 5 PCR amplification cycles for inputs.

tag: antibody

value: Wapl


title: ChIPseq_ESC_Wapl_IP_BPTFko_rep1

tag: cell type


title: PFC, Saline, rep5


title: G3M,CON,H3K27ac_SI_rep2


title: G3M,CON,H3K27ac_SI_rep1


title: PFC, Saline, rep4


title: SKNAS-GAC-002

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60) and were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation ( human release 31).
Assembly: GRCh38(hg38)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: SKNAS

growth_protocol: BE2C and SK-N-AS were cultured in 1X RPMI1640 (Corning, 425 15-040-CV) supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich, F2442), 1% L-Glutamine 426 (Corning, A2916801).

extract_protocol:
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: BE2C and SKNAS were transduced with Lenti virus control, GAC and KGA to overexpression GCA and KGA.

value: SKNAS

value: Neuroblastoma

value: GAC-overexpression


title: PFC, Saline, rep3


title: ChIPseq_ESC_Wapl_IP_wt_rep2


title: ChIPseq_ESC_Rad21_input_BPTFko_rep3

value: BPTF knock-out


title: ChIPseq_ESC_Rad21_input_BPTFko_rep1


title: SKNAS-GAC-001


title: Ventral tissue at E11.5, biological rep 1

type: RNA

city: Paris

first: Charles

last: Durand

address: 9, quai saint-Bernard

description: Gene expression data from ventral aortic  tissue at E11.5

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. RMA normalization is performed using R with Version 19 of Entrezgene CDF brain array.

label: biotin

source_name: Ventral tissue at E11.5

label_protocol: Between 200 and 1000 pg of total RNA was reverse transcribed following the Ovation Pico V2 system (Nugen) and the resulting double strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, sens target DNA was fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

growth_protocol: Embryos were collected from pregnant C57B/6 mice at embryonic day 11.5.

extract_protocol: Microdissected tissues were collected on appropriate caps and then proceeded for RNA extraction using Acturus Picopure RNA isolation kit. RNAs were eluted in a final volume of 13 μl and their concentrations and integrity quantified on a bioanalyzer (Agilent).

treatment_protocol: Unfixed embryos were embedded in OCT medium in presence of isopentane cooled at -65°C. Twenty μm cryostat sections were then prepared and stained before laser micro-dissection. The dorsal tissue localized in between the notochord and the roof of the aorta and the ventral tissue underneath the aorta were isolated from the same embryos.

value: ventral aortic tissue

tag: isolation

value: Tissue isolated by laser microdissection

tag: developmental stage


title: Ventral tissue at E11.5, biological rep 2


title: ChIPseq_ESC_Rad21_input_BPTFko_rep2

value: embryonic stem cells


title: Dorsal tissue at E11.5, biological rep 2

description: Gene expression data from dorsall aortic  tissue at E11.5

source_name: Dorsal tissue at E11.5

value: dorsal aortic tissue


title: ChIPseq_ESC_Wapl_IP_BPTFko_rep2


title: PFC, PICK1i, rep3

tag: treatment


title: Dorsal tissue at E11.5, biological rep 3


title: ChIPseq_ESC_Rad21_input_wt_rep3


title: Dorsal tissue at E11.5, biological rep 1


title: SKNAS-KGA-001

value: KGA-overexpression


title: ChIPseq_ESC_Rad21_input_wt_rep2


title: Ventral tissue at E11.5, biological rep 3


title: PFC, Saline, rep2


title: NPC, short read, light polyribosome (2-4 ribosomes), rep1

city: San Francisco

first: Julie

last: Zikherman

address: 513 Parnassus Ave

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, San Francisco

data_processing:
Long read FASTQs: Bonito v0.0.1 (basecalling) and Mandalorion v4.0.0 (high confidence consensus sequence definition and transcriptome assembly)
Long read data analysis: SQANTI3 v5.1.1 (transcriptome QC and filtering) and IsoAnnot Lite v.2.7.3 (transcriptome annotation)
Short read data analysis: STAR v2.7.8a (mapping to the genome and to the transcriptome), Salmon v1.9.0 (alignment to the transcriptome) and tappAS v1.0.7 (differential and functional analyses)
Supplementary files format and content: Supplementary_tables.xlsx, contains: short read and long read library/mapping stats, transcriptome feature annotations and raw counts, differential isoform usage analysis results, alternative splicing analysis results and motif analysis results.
Supplementary files format and content: LR_transcriptome.gtf: de novo transcriptome from the long read libraries, made and filtered with Mandalorion and SQANTI3.

extract_protocol:
BIOO Scientific qRNA
BIOO qRNA seq v2  Library Preparation Kit  -- strand-specific, read1 is antiSense to input RNA
Frac-seq

value: neural progenitor cell (NPC)

value: dual-SMAD inhibition

tag: fraction

value: light polyribosome (2-4 ribosomes)

tag: riborna depletion

value: poly A+

tag: pcr


title: NPC, short read, heavy polyribosome (5+ ribosomes), rep3

tag: cell line

value: heavy polyribosome (5+ ribosomes)


title: SKNAS-Ctr-002

value: control


title: ChIPseq_ESC_Rad21_input_wt_rep1

tag: genotype

value: wild-type


title: SKNAS-Ctr-001


title: ChIPseq_ESC_Rad21_IP_BPTFko_rep3


title: PFC, PICK1i, rep4

value: PFC


title: PFC, Saline, rep1

value: Saline


title: PFC, PICK1i, rep2


title: NPC, short read, light polyribosome (2-4 ribosomes), rep3


title: NPC, short read, heavy polyribosome (5+ ribosomes), rep2


title: NPC, short read, heavy polyribosome (5+ ribosomes), rep1


title: BE2C-GAC-002

value: Neuroblastoma


title: BE2C-GAC-001

value: GAC-overexpression


title: ChIPseq_ESC_Rad21_IP_BPTFko_rep1

value: BPTF knock-out


title: ChIPseq_ESC_Rad21_IP_BPTFko_rep2


title: NPC, short read, monosome, rep3

value: monosome


title: NPC, short read, light polyribosome (2-4 ribosomes), rep2


title: PFC, PICK1i, rep1


title: SKNAS-KGA-002

value: SKNAS


title: BE2C-KGA-002


title: NPC, short read, monosome, rep2


title: ChIPseq_ESC_Rad21_IP_wt_rep3

value: embryonic stem cells


title: BE2C-KGA-001


title: ChIPseq_ESC_Rad21_IP_wt_rep2


title: BE2C-Ctr-002


title: ChIPseq_ESC_Rad21_IP_wt_rep1


title: BE2C-Ctr-001


title: ChIPseq_ESC_CTCF_input_BPTFko_rep4


title: NPC, short read, monosome, rep1


title: NPC, short read, cytosol, rep3

value: cytosol


title: NPC, short read, cytosol, rep2


title: ChIPseq_ESC_CTCF_input_BPTFko_rep3


title: NPC, short read, cytosol, rep1


title: ChIPseq_ESC_CTCF_input_wt_rep4


title: ESC, short read, light polyribosome (2-4 ribosomes), rep3

value: embryonic stem cell (ESC)


title: ChIPseq_ESC_CTCF_IP_BPTFko_rep4

value: CTCF


title: Control_31

city: Seoul

first: Sung Wan

last: Kang

address: 88, Olympic-ro 43-gil, Songpa-gu

institute: Asan Medical Center

data_processing:
Trimmomatic v0.38 was utilized to remove adapter sequences and trim bases with subpar quality before analysis.
The refined reads were aligned to the Homo sapiens (GRCh38) genome using HISAT v2.1.0, based on the HISAT and Bowtie2 implementations.
The aligned data, in SAM file format, were sorted and indexed using SAMtools v1.9.
StringTie v2.1.3b was employed for the assembly and quantification of transcripts after alignment.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-delimited text file includes TPM values for each sample

source_name: Tumor

extract_protocol:
Total RNA was isolated from the tumor tissues of SKOV-3 Luc xenograft in Hu-mice treated with either PBS or pembrolizumab. The isolation was performed using the mirVana miRNA isolation kit (Thermo Fisher Scientific).
A library was prepared with 100 ng of total RNA for each sample using the TruSeq RNA Access library prep kit (Illumina).

value: Tumor

value: Cancer cells

value: PBS


title: Pembro_19

value: Pembrolizumab


title: ChIPseq_ESC_CTCF_input_wt_rep3


title: ESC, short read, light polyribosome (2-4 ribosomes), rep2

value: control

value: light polyribosome (2-4 ribosomes)

value: poly A+


title: ESC, short read, light polyribosome (2-4 ribosomes), rep1


title: Control_21


title: ChIPseq_ESC_CTCF_IP_BPTFko_rep3


title: ESC, short read, heavy polyribosome (5+ ribosomes), rep3

value: heavy polyribosome (5+ ribosomes)


title: Pembro_36


title: ChIPseq_ESC_CTCF_IP_wt_rep4

value: wild-type


title: Epi4

city: Shanghai

first: yujuan

last: jin

address: Yueyang Road 320#

institute: Shanghai Institutes for Biological Sciences, CAS

hyb_protocol: Each slide was hybridized with 1.65mg Cy3-labeled cRNA using Gene Expression Kit (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

scan_protocol: After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instructions. Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution = 5 mm, PMT 100%, 16 bits.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). GSEA was performed following the developer’s protocol (http://www.broad.mit.edu/gsea/).

source_name: non-NE small cell lung cancer

label_protocol: Total RNAs were amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

extract_protocol: Total RNAs from the Mes and Epi cell lines were extracted by TRIzol reagent (Life Technologies) according to the manufacturer’s instruction.

treatment_protocol: no treatment

value: Epi cell line

tag: genetic backgroud

value: RbL/L, Trp53L/L


title: ESC, short read, heavy polyribosome (5+ ribosomes), rep2