title: Tepotinib-treated, ROI 006


title: Tepotinib-treated, ROI 009

status: Public on Sep 27 2024

type: protein

city: Darmstadt

first: Manon

middle: A

last: Simard

address: Frankfurterstraße 250

department: Research Unit Oncology

country: Germany

institute: Merck Healthcare KGaA

description:
20231006_P1001660003346A_P1001660003346A_12.RCC
DNA barcode cleaved from RNA probe

scan_protocol: Scanned using the GeoMx DSP (NanoString Technologies)

data_processing: For an nCounter readout, the collected samples were first hybridized overnight to the GeoMx Hyb Code master mixes, consisting of probes U and R in hybridization buffer, as outlined in the GeoMx nCounter protein readout user guide. Hybridization products were then pooled for readout on the MAX/FLEX nCounter system. RCC files were loaded back onto the GeoMx instrument for downstream analysis in the GeoMx Analysis Suite.

molecule: protein

organism: Homo sapiens

source_name: METex14 NSCLC

label_protocol: Following BOND Rx protocol, slides were incubated overnight at 37 ˚C with the selected protein panels: Immune Cell Profiling, Immune Cell Typing, Immune Activation Status, IO Drug Targets, PI3K/AKT Signaling; as well as the morphology markers: TTF1, CD3 and CD33. The following day, post-fixation of section was performed, after washing the slides 3 times in TBS-T for 10 minutes, using 4% paraformaldehyde in a humidity chamber for 30 minutes. Slides were then washed twice for 2 minutes in TBS-T. Nuclear staining was then performed in a humidity chamber using SYTO13 DNA stain for 15 minutes. Slides were finally washed twice in TBS-T before being loaded into the GeoMx DSP instrument.

growth_protocol: FFPE blocks, tepotinib-treated surgical resection was obtained following 42 days of tepotinib treatment

treatment_protocol: The slide preparation was performed as per GeoMx DSP Slide Preparation Protocol using the Semi-Automated BOND Rx protocol. In brief, 5 µm tissue sections were positioned in the GeoMx imaging area on a SuperFrost Plus slide. Sections were incubated at 60 ˚C for over 30 minutes prior to BOND Rx protocol. BOND Rx protocol consisted of Bake & Dewax, HIER for 20 minutes with ER1.

tag: Sex

value: female

tag: tumor type

value: NSCLC

tag: mutation

tag: tnm

tag: ttf1 staining

value: positive

tag: tissue

value: Tumor


title: Tepotinib-treated, ROI 010

description:
20231006_P1001660003346A_P1001660003346A_01.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 007

description:
20231006_P1001660003346A_P1001660003346A_10.RCC
DNA barcode cleaved from RNA probe


title: L840

type: SRA

city: Munich

first: Laurenz

middle: Thomas

last: Ursch

address: Trogerstraße 30

institute: TUM

library_source: genomic

data_processing:
Screening for deletion using CRISPResso2 (V2.2.7)
Reads for each deletion were normalised and displayed in a cumulative way
Assembly: hg38
Supplementary files format and content: .txt file with the range of deletions
Library strategy: Amplicon-Sequencing

molecule: genomic DNA

growth_protocol: PBMCs were enriched for CD4 or CD8 T cells usingMojoSortHuman CD4 T Cell Isolation Kit (Biolegend) or MojoSort™ Human CD8 T Cell Isolation Kit (Biolegend), respectively. The freshly obtained T cells were cultured in complete Roswell Park Memorial Institute (cRPMI) medium, consisting of RPMI 1640 (ThermoFisher) supplemented with 5 mmol/l HEPES (ThermoFisher), 2 mmol/l glutamine (ThermoFisher), 50 µg/ml penicillin/streptomycin (ThermoFisher), 5 mmol/l nonessential amino acids (ThermoFisher), 5 mmol/l sodium pyruvate (ThermoFisher) and 10% FBS (Sigma-Aldrich) at a concentration of 1x106cells/ml for 24 - 48 hrs at 37°C before Cas9 RNP nucleofection.

extract_protocol:
cells were resuspended in DNA Quick Extraction solution (Lucigen) to lyse the cells and extract genomic DNA. The cell lysate was incubated at 65 °C for 5 min, then 95 °C for 5 min, and stored at −20 °C.
A 25 µl PCR-reaction contained 10 µl of genomic DNA, 0.5 µl 10 µM primer forward, 0.5 µl 10 µM primer reverse,  12.5 µl 2x GoTaq Long PCR Master Mix (Promega) and 1.5 µl H2O. The thermocycler setting consisted of one step at 95 °C for 1 min; followed by 18 cycles at 98°C for  10 s, 65°C for 15 s and 72°C for 15 s (wherein the annealing temperature was decreased by 0.5 °C per cycle); followed by 15 cycles at 98°C for 10 s, 58°C for 15 s and 72°C for 15 s; with one final step at 72°C for 5 min. The PCR products were cleaned up using AMPure beads according to the manufacturer's recommendations (Beckmann Coulter) and eluted in 50 µl 10 mM Tris. For barcoding, 2 µl of the purified DNA were added to 10 µl of 2x GoTaq Long PCR Master Mix, 2 µl of Nextera XT index 1 (i7) primer, 2 µl of Nextera XT index 2 (i5) primer (Illumina) and 4 µl of H2O. The PCR reactions were heated up to 95 °C for 3 min, followed by 8 cycles of 95°C for  30 s, 55°C for 30 s and 72°C for 30 s and a further elongation step for 5 min at 72°C. The second PCR products were again purified with AMPure beads and eluted in  27.5 µl 10 mM Tris. Cleaned-up PCR products were quantified using the SpectraMax Quant AccuBlue HighRange dsDNA Kit (Molecular Devices) on the SpectraMax 3x instrument (Molecular Devices). Equal amounts of DNA/sample were pooled and sequenced on an Illumina MiSeq instrument (Illumina) with a MiSeq Reagent Nano Kit v2 (500-cycles) (Illumina) according to the manufacturer’s recommendations.

treatment_protocol: 80 µM crRNA (IDT) and 80µMtracrRNA(IDT) were mixed in a 1:1 ratio and incubated for 5 min at 96°C to generate 40 µMcrRNA:tracRNA duplexes (gRNA sequences: Suppl. Table 1). An equal volume of 40 µM Streptococcus pyrogenes Cas9-NLS (made in-house;59; Cas9 expression plasmid pMJ915 (Addgene)) was carefully added to the crRNA-tracrRNAduplex and incubated for 20 min at room temperature (RT) to generate 20 µM Cas9 RNPs. 1x106cells were resuspended in 20 µl P3 buffer with Supplement 1 (LONZA) and 4 µl 20 µM Cas9 RNP and 1 µl of100 µM electroporation enhancer (Sigma-Aldrich) were added. T cells were nucleofected in 96 well reaction cuvettes (LONZA) using program EH-115 on theLonza 4D-Nucleofector (LONZA). Directly after nucleofection, 80 µlcRPMIwere added to the reaction cuvette. After resting for 30 min at 37°C the cells were transferred to a 96 well-plate and either activated withDynabead Human T-Activator CD3/CD28 (ThermoFisher) in a cell: bead ratio of 10:1 and cultured with 100 U/ml IL-2 (Peprotech) or cultured with 0.5 ng/ml IL-7 (Peprotech) and 0.5 ng/ml IL-15 (Peprotech) (“non-activated” T cells). IL-2 was replenished on day 6 of culture. 0.5 µM PFT-µ (Sigma) or 30 µM cyclic PFT-α (Hölzel Diagnostika) were added directly after nucleofection in the resting medium, as well as in the cultivation medium.

value: PBMCs

tag: cell type

tag: genotype


title: L839


title: L838


title: Tepotinib-treated, ROI 002

description:
20231006_P1001660003346A_P1001660003346A_05.RCC
DNA barcode cleaved from RNA probe


title: Pre-treatment, ROI 015

description:
20231006_P1001660003346A_P1001660003346A_03.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 004

description:
20231006_P1001660003346A_P1001660003346A_07.RCC
DNA barcode cleaved from RNA probe


title: Tepotinib-treated, ROI 001

description:
20231006_P1001660003346A_P1001660003346A_04.RCC
DNA barcode cleaved from RNA probe


title: L849


title: L835


title: L834


title: L833


title: L836


title: L832


title: Pre-treatment, ROI 012

value: negative

value: Periphery


title: Pre-treatment, ROI 013


title: Pre-treatment, ROI 011

description:
20231006_P1001660003346A_P1001660003346A_11.RCC
DNA barcode cleaved from RNA probe


title: Pre-treatment, ROI 010


title: L831


title: Pre-treatment, ROI 009

description:
20231006_P1001660003346A_P1001660003346A_09.RCC
DNA barcode cleaved from RNA probe


title: L829


title: L828


title: L830


title: Tepotinib-treated, ROI 005

description:
20231006_P1001660003346A_P1001660003346A_08.RCC
DNA barcode cleaved from RNA probe


title: L827


title: Tepotinib-treated, ROI 003

description:
20231006_P1001660003346A_P1001660003346A_06.RCC
DNA barcode cleaved from RNA probe


title: Pre-treatment, ROI 007


title: Pre-treatment, ROI 005


title: L837


title: L826


title: Pre-treatment, ROI 008


title: Pre-treatment, ROI 006


title: L825


title: Pre-treatment, ROI 004


title: L824


title: Pre-treatment, ROI 014

description:
20231006_P1001660003346A_P1001660003346A_02.RCC
DNA barcode cleaved from RNA probe


title: Pre-treatment, ROI 003


title: Pre-treatment, ROI 001


title: L822


title: L821


title: L820


title: L755

tag: concentration

tag: treatment

value: PFTu


title: Tepotinib-treated, ROI 078

type: other

description:
Sex: female; Tumor type: NSCLC; Mutation: METex14; TNM: ypT1aN0M0; TTF1 staining:  negative
DNA barcode cleaved from RNA probe

hyb_protocol: Overnight at 37˚C for RNA probes

data_processing: Sequencing libraries were generated as per NanoString Technologies protocol. First, unique i5 and i7 sample indices were added to the oligonucleotide barcodes by PCR (4 µL of extracted barcode oligonucleotides + 4 µL of indexing primers + 2 µL of NanoString 5X PCR master mix per reaction). PCR protocol: 37˚C for 30 min; 50˚C for 10 min; 95˚C for 3 min; 18 cycles of 95˚C for 15 s, 65˚C  for 1 min, 68˚C for 30s; 68˚C  for 5 min. PCR products were pooled and purified twice with AMPure XP beads (Beckman Coulter). Purified pooled libraries were sequenced on an Illumina NovaSeq6000, paired-end 2x27 base pairs with unique dual indices workflow. FASTQ files were derived then converted to digital count conversion (DCC) files for uploading to the GeoMx analysis suite.

label: Periphery

molecule: other

label_protocol: Following BOND Rx protocol, slides were hybridized overnight at 37 ˚C with the Cancer Transcriptome Atlas and selection custom probes, covered with HybriSlip Hybridization covers. The following day, covers were removed and two 25 minute stringent washes were performed in 2X Saline Sodium Citrate (SSC) buffer with 50% formamide followed by two 5 minute washes in SSC. Sections were then placed in a humidity chamber for blocking with buffer W for 30 minutes, followed by morphology marker staining with SYTO13, TTF1, CD3 and CD33 for 1 hour. Slides were washed with SSC twice and loaded into the GeoMX DSP for region of interest selection and barcode collection.

extract_protocol: none provided

treatment_protocol: The slide preparation was performed as per GeoMx DSP Slide Preparation Protocol using the Semi-Automated BOND Rx protocol. In brief, 5 µm tissue sections were positioned in the GeoMx imaging area on a SuperFrost Plus slide. Sections were incubated at 60 ˚C for over 30 minutes prior to BOND Rx protocol. BOND Rx protocol consisted of Bake & Dewax, HIER for 20 minutes with ER2 and 15 minute incubation with Protease K (1 µg/mL), followed by post-fixation in 10% neutral buffered formalin (NBF) for 5 minutes and then washed twice in  NBF stop buffer (0.1M Tris Base, 0.1M Glycine).


title: Tepotinib-treated, ROI 079

description:
Sex: female; Tumor type: NSCLC; Mutation: METex14; TNM: ypT1aN0M0; TTF1 staining:  positive
DNA barcode cleaved from RNA probe

label: Tumor


title: L751

value: PFTa


title: L754


title: L753


title: L752


title: L748


title: L749


title: L750


title: Tepotinib-treated, ROI 073


title: Tepotinib-treated, ROI 074


title: L747


title: Pre-treatment, ROI 002


title: L823


title: Tepotinib-treated, ROI 072


title: Tepotinib-treated, ROI 071


title: Tepotinib-treated, ROI 070


title: L746


title: L745


title: Tepotinib-treated, ROI 068


title: Tepotinib-treated, ROI 069


title: Tepotinib-treated, ROI 066


title: Tepotinib-treated, ROI 067


title: L744


title: Tepotinib-treated, ROI 076


title: Tepotinib-treated, ROI 077


title: L743


title: Tepotinib-treated, ROI 075


title: L742


title: Tepotinib-treated, ROI 065


title: L741


title: L740


title: Tepotinib-treated, ROI 064


title: Tepotinib-treated, ROI 063


title: Tepotinib-treated, ROI 062


title: L739


title: L738


title: L736


title: L735


title: Tepotinib-treated, ROI 058


title: Tepotinib-treated, ROI 060


title: Tepotinib-treated, ROI 059


title: L734


title: L732


title: Tepotinib-treated, ROI 057


title: L730


title: L729


title: Tepotinib-treated, ROI 054


title: Tepotinib-treated, ROI 055


title: Tepotinib-treated, ROI 056


title: L731


title: L728


title: Tepotinib-treated, ROI 051


title: Tepotinib-treated, ROI 053


title: Tepotinib-treated, ROI 061


title: Tepotinib-treated, ROI 052


title: L727


title: Tepotinib-treated, ROI 050


title: L725


title: L737


title: Tepotinib-treated, ROI 048


title: Tepotinib-treated, ROI 046


title: Tepotinib-treated, ROI 047


title: L724


title: L733


title: L722


title: L723


title: Tepotinib-treated, ROI 045


title: L721


title: Tepotinib-treated, ROI 043


title: Tepotinib-treated, ROI 042


title: L554


title: Tepotinib-treated, ROI 049


title: L553


title: Tepotinib-treated, ROI 044


title: L720


title: Tepotinib-treated, ROI 041


title: L549


title: Tepotinib-treated, ROI 038


title: Tepotinib-treated, ROI 040


title: L550


title: L551


title: L726


title: L552


title: Tepotinib-treated, ROI 039


title: Tepotinib-treated, ROI 037


title: Tepotinib-treated, ROI 036


title: Tepotinib-treated, ROI 035


title: L547


title: L545


title: L546


title: Tepotinib-treated, ROI 034


title: L542


title: L548


title: Tepotinib-treated, ROI 031


title: Tepotinib-treated, ROI 032


title: Tepotinib-treated, ROI 033


title: L541


title: L539


title: L540


title: L536


title: Tepotinib-treated, ROI 028


title: Tepotinib-treated, ROI 029


title: L535


title: Tepotinib-treated, ROI 027


title: L534


title: Tepotinib-treated, ROI 026


title: L533


title: Tepotinib-treated, ROI 025


title: L529


title: Tepotinib-treated, ROI 024


title: Tepotinib-treated, ROI 023


title: L528


title: Tepotinib-treated, ROI 022


title: L526


title: Tepotinib-treated, ROI 030


title: L525


title: Tepotinib-treated, ROI 021


title: L523


title: L522


title: Tepotinib-treated, ROI 018


title: Tepotinib-treated, ROI 020


title: Tepotinib-treated, ROI 019


title: L519


title: L520


title: Tepotinib-treated, ROI 015


title: Tepotinib-treated, ROI 016


title: L518


title: L530


title: L515


title: L514


title: L507


title: Tepotinib-treated, ROI 013


title: L506


title: L503


title: Tepotinib-treated, ROI 011


title: Tepotinib-treated, ROI 010


title: Tepotinib-treated, ROI 017


title: L501


title: L502


title: L499


title: Tepotinib-treated, ROI 007


title: Tepotinib-treated, ROI 006


title: Tepotinib-treated, ROI 009


title: L493


title: L492


title: L488


title: L491


title: Tepotinib-treated, ROI 014


title: Tepotinib-treated, ROI 012


title: Tepotinib-treated, ROI 004


title: Tepotinib-treated, ROI 005


title: Tepotinib-treated, ROI 002


title: Tepotinib-treated, ROI 003


title: L486


title: Pre-treatment, ROI 015

description:
Sex: female; Tumor type: NSCLC; Mutation: METex14; TNM: cT3N2M0; TTF1 staining:  positive
DNA barcode cleaved from RNA probe


title: Pre-treatment, ROI 014


title: L485


title: Tepotinib-treated, ROI 008


title: L495


title: Pre-treatment, ROI 013


title: L482


title: L480


title: L481


title: L479


title: L487


title: L471


title: L472


title: L469


title: L476


title: Tepotinib-treated, ROI 001


title: L474


title: L475


title: ATAC-seq_P3_male_DcKO_rep2

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

country: USA

institute: University of California, Davis

data_processing:
Raw paired-end ATAC-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to either the mouse (GRCm38/mm10) genomes using bowtie2 (version 2.3.3.1) with default arguments.
The aligned reads were filtered to remove alignments mapped to multiple locations by calling grep with the -v option before being subjected to downstream analyses.
PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute).
Biological replicates were pooled for visualization and other analyses after validation of reproducibility.
Peak calling for ATAC-seq data was performed using MACS3 (version 3.0.0a7) with default arguments.
Assembly: mm10
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: testis

extract_protocol:
FACS-sorted cells were isolated from P1 ovaries or P3 testis and pooled as one replicate. Samples were lysed in 50 μl of lysis buffer (10 mM Tris–HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) on ice for 10 min. Immediately after lysis, nuclei were spun at 500 × g for 10 min at 4 °C to remove the supernatant.
Nuclei were then incubated 10 μl of transposition mix (0.5 µl homemade Tn5 transposase, 5 µl 2× TD buffer (10 mM Tris–HCl (pH 7.6), 10 mM MgCl2, and 20% Dimethyl Formamide), 3.3 µl PBS, 0.1 μl 1% digitonin, 0.1 μl 10% Tween-20, and 1 μl water) at 37 °C for 30 min in a thermomixer with shaking at 500 rpm.
the transposed DNA was purified with a MinElute kit (Qiagen). DNA libraries were prepared through the omni-ATAC method (PMID: 28846090)

tag: strain

value: C57BL/6 X 129S1/Sv X FVB/NJ

value: testis

value: Undifferentiated Spermatogonia

value: Chd4 f/-; Ddx4-Cre Tg/+

tag: age

value: postnatal day 3


title: L466


title: ATAC-seq_P3_male_DcKO_rep1


title: L463


title: L461


title: ATAC-seq_P3_male_Dctrl_rep1

value: Chd4 f/+; Ddx4-Cre Tg/+


title: L468


title: ATAC-seq_P3_male_Dctrl_rep2


title: L462


title: CUTTag_CHD4_P1_NGO_Chd4f/f_rep1

data_processing:
Raw paired-end CUT&Tag reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to either the mouse (GRCm38/mm10) genomes using bowtie2 (version 2.3.3.1) with default arguments.
The aligned reads were filtered to remove alignments mapped to multiple locations by calling grep with the -v option before being subjected to downstream analyses.
PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute).
Biological replicates were pooled for visualization and other analyses after validation of reproducibility.
Peak calling for CUT&Tag data was performed using MACS3 (version 3.0.0a7) with default arguments.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: ovary

extract_protocol:
FACS-sorted cells were isolated from P1 Chd4 f/f ovaries.
CUT&Tag libraries of P1 oocytes for CHD4 were generated according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017).

value: ovary

value: Non-growing oocytes

value: Chd4 f/f

value: postnatal day 1

tag: antibody

value: mouse anti-CHD4 (Abcam; ab70469)


title: L459


title: L458


title: L456


title: Poly(I:C) treated mice

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: 15K cells loaded

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the mouse genome (mm10, Ensembl 93) using CellRanger workflow, and samples passing QC were normalized and aggregated with CellRanger aggr.
Assembly: mm10
Supplementary files format and content: Filtered gene h5 output from CellRanger

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Lineage (TER-119, CD19, B220, TCRbeta, NK1.1, Siglec-f, F4/80) -negative, FLT3+ cells from the spleen were suspended in 50 ul of 1.0% BSA.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines NEXT GEM Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 12 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina High Seq to approximate the number of recovered cells in each sample.

treatment_protocol: Mice were treated with either PBS or Poly(I:C) 24 hours prior to euthanization and spleen collection

value: Spleen


title: PBS treated mice

description: 15K cells loaded


title: Poly(I:C) treated mice (1:1)

description: 15K cells loaded

extract_protocol:
Pan-DC enriched cells (EasySep, StemCell Technologies) and CD45+ cells (EasySep Release PE positive selection kit) were mixed at a 1:1 ratio before loading on the 10X platform
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines NEXT GEM Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 12 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina High Seq to approximate the number of recovered cells in each sample.


title: CUTTag_CHD4_P1_NGO_Chd4f/f_rep2


title: L460

value: PBMCs


title: L454


title: L452


title: L451


title: L450


title: MKOS_MEF, 0h, empty_ctrl, ATAC-seq, rep_2

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
The contaminating ME sequences (CTGTCTCTTATACACATCT) were trimmed from the ATAC-seq reads with Cutadapt to prevent multimapping.
The ATAC-seq pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated alignments were removed using Picard (https://broadinstitute.github.io/picard/).
ATAC-seq reads (bam files) from different replicates were merged and then normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters.
Assembly: mm9
Supplementary files format and content: bigwig files showing sequence depth normalized ATAC-seq enrichment of the merged data.

growth_protocol: Early passage (passage 1) mouse embryonic fibroblasts (MEFs) were cultured for 48hr in MEF medium (GMEM medium supplemented with 10% FCS, 1 mM sodium pyruvate, 1 mM glutamine, and 5.7 ml MEM 100X Non-Essential Amino Acids Solution, 50 M 2-mercaptoethanol (Gibco, Thermo Fisher Scientific) at 37C and 5% CO2.

extract_protocol:
50,000 of freshly harvested cells were resuspended in ice-cold RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2). The suspension was centrifuged at 500xg for 3 min using a refrigerated centrifuge. The cell pellet was washed once with 50 μl ice-cold PBS and centrifuged at 500xg for 3 min at 4°C. The cell pellet was resuspended in ice-cold Lysis Buffer (48.5 μl RSB buffer supplemented with 0.5 μl of 10% NP-40, 0.5 μl of 10% Tween-20, 0.5 μl of 1% Digitonin) and kept on ice for 3 min. Then, 1 ml of wash buffer (RSB buffer supplemented with 0.1% Tween-20) was added on the lysed cells. Nuclei were pelleted at 500xg for 10 min at 4°C and the supernatant (cytoplasm fraction) was carefully discarded. The nuclei were resuspended in the transposition mix (25 μl of 2X Tagment DNA Buffer (Illumina, #20034197), 16.5 μl of 1X PBS, 0.5 μl 10% of Tween-20, 0.5 μl of 1% Digitonin, 5 μl nuclease-free H2O). Next, 2.5 μl of Tn5 Transposase (Illumina, #20034197) was added to the reaction mix by pipetting up and down 6 times. The reaction was then incubated at 37℃ for 30 minutes on a thermomixer at 1,000 rpm. Finally, the tagmented DNA was isolated using Qiagen MinElute Reaction Cleanup Kit (Qiagen, # 28204) following the manufacturer’s instructions.
ATAC-seq libraries were generated by PCR amplification using custom-made barcodes (Buenrostro et al., 2013). Libraries were amplified with 7-10 cycles using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541S). To remove primer dimers and DNA fragments shorter than 150bp, libraries were purified with SpeedBeads™ beads. 1.8X volume of SpeedBeads™ beads (81 μl beads for 45 μl PCR reaction) was used to clean PCR amplified DNA library. The quality of the DNA libraries was assessed using Agilent HS DNA Screen Tape (Agilent. Santa Clara, CA). The concentration of the DNA libraries was measured by Qubit Fluorometric Quantitation. Equimolar DNA libraries were pooled to a final concentration of 2 nM. The ATAC-seq libraries were sequenced by Novagene (Novogene, UK) on Illumina HiSeq 2500 using pair-ends PE150 in biological duplicates (Illumina, San Diego, CA).

treatment_protocol: MEFs or MKOS-MEFs were infected with lentiviruses to over express the linker histon  H1 (H1OE), or knockdown H1 expression (H1KD).

tag: cell line

value: Secondary dox-inducible MKOS mouse embryonic fibroblasts

value: No Dox, infected with empty vector lentivirus ctrl


title: endothelial cells，control

city: nantong

first: wang

last: xiaoning

state: jiangsu

address: Qixiu Road 19

country: China

institute: Nantong University

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger 3.0.2 (https://github.com/10XGenomics/cellranger) was used to convert the raw sequencing data to single-cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 (https://satijalab.org/seurat/install.html)
Assembly: The reference genome (fasta format) and gene annotation (gtf format) files were downloaded from Ensembl database (release version 94).
Supplementary files format and content: Tab-separated values files and matrix files.

molecule: total RNA

organism: Danio rerio

source_name: endothelial cells

growth_protocol: Tg(kdrl:EGFP) embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.

extract_protocol:
Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline (PBS) containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. After centrifuging for 5 min at 800 g at 4°C, cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum (FCS) to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS.
EGFP positive cells were first enriched by fluorescence-activated cell sorting (FACS), and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.

treatment_protocol: Embryos were treated with 6% glucose from 24 to 72 hpf.

value: endothelial cells


title: MKOS_MEF, 72h, H1OE, ATAC-seq, rep_2

value: Dox for 72h, infected with lentivirus overexpressing linker H1


title: endothelial cells，high glucose

description: 10x genomics


title: L457

value: PFTa


title: L455


title: L361


title: PBS treated mice (1:1)

description: 15K cells loaded


title: L453


title: L360


title: MKOS_MEF, 72h, empty_ctrl, ATAC-seq, rep_2

value: Dox for 72h, infected with empty vector lentivirus ctrl


title: MKOS_MEF, 0h, H1KD, ATAC-seq, rep_1

value: No Dox, infected with shRNA lentivirus targeting linker H1


title: MKOS_MEF, 0h, empty_ctrl, ATAC-seq, rep_1


title: L367


title: MKOS_MEF, 72h, ATAC-seq, rep_1

value: Dox for 72h


title: L338


title: Pre-treatment, ROI 003

description:
Sex: female; Tumor type: NSCLC; Mutation: METex14; TNM: cT3N2M0; TTF1 staining:  negative
DNA barcode cleaved from RNA probe

value: NSCLC


title: Pre-treatment, ROI 001


title: Pre-treatment, ROI 002


title: L355


title: L363


title: MKOS_MEF, 72h, H1OE, ATAC-seq, rep_1


title: L362


title: MKOS_MEF, 72h, empty_ctrl, ATAC-seq, rep_1


title: MKOS_MEF, 72h, H1KD, ATAC-seq, rep_2

value: Dox for 72h, infected with shRNA lentivirus targeting linker H1


title: MKOS_MEF, 72h, H1KD, ATAC-seq, rep_1


title: MEF, H1OE, ATAC-seq, rep_4

source_name: MEF

value: MEF

value: mouse embryonic fibroblasts

value: infected with lentivirus overexpressing linker H1


title: MKOS_MEF, 0h, H1KD, ATAC-seq, rep_2


title: L359


title: L332


title: L333


title: L339


title: MKOS_MEF, 72h, ATAC-seq, rep_2


title: L329


title: MKOS_MEF, 0h, ATAC-seq, rep_2

value: No Dox


title: L336


title: Pre-treatment, ROI 008


title: Pre-treatment, ROI 010


title: Pre-treatment, ROI 009


title: Pre-treatment, ROI 012


title: Pre-treatment, ROI 005


title: Pre-treatment, ROI 011


title: Pre-treatment, ROI 006


title: Pre-treatment, ROI 004


title: Pre-treatment, ROI 007


title: L335


title: MKOS_MEF, 0h, ATAC-seq, rep_1


title: MEF, H1KD, ATAC-seq, rep_2

value: infected with shRNA lentivirus targeting linker H1


title: L321


title: MEF, H1KD, ATAC-seq, rep_1


title: MEF, empty vector control, ATAC-seq, rep_4

value: infected with empty vector lentivirus


title: MEF, H1OE, ATAC-seq, rep_3


title: MEF, H1OE, ATAC-seq, rep_2


title: L331

value: PBMCs


title: MEF, H1OE, ATAC-seq, rep_1


title: MEF, H1KD, ATAC-seq, rep_4


title: MEF, empty vector control, ATAC-seq, rep_1


title: MEF, H1KD, ATAC-seq, rep_3


title: Cortex, 19-month old, Gde2KO1

city: Baltimore

first: Shanthini

last: Sockanathan

state: Maryland

address: PCTB1004, 725 North Wolfe Street

department: Neuroscience

institute: The Johns Hopkins University School of Medicine

data_processing:
Illumina's bcl2fastq 2.17 software
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
Trimmed reads from 19-month samples were mapped to GRCm38 genome using STAR aligner v.2.5.2b. The subsequent .bam files were used as input for Leafcutter.
For differential expression, reads from both 4-month and 19-month samples were mapped to GRCm38 transcriptome using Kallisto.
Kallisto outputs were analyzed using Sleuth for readcounts and normailization.
Assembly: GRCm38
Supplementary files format and content: csv files containing transcript level TPM and normalized est_counts for each sample
Supplementary files format and content: csv files containing sample information and feature information.

source_name: brain, cortex

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions

value: brain, cortex


title: L323


title: L314


title: L322


title: L315


title: L324


title: 15U Mnase MicroC, MEF-H1KD

description: MEFs overexpressing linker histone H1

data_processing:
Micro-C reads were aligned to mm9 and processed using the Nextflow pipeline distiller-nf.
The aligned Micro-C data were processed using the Nextflow (https://www.nextflow.io/) pipeline distiller-nf (https://github.com/open2c/distiller-nf) using following configurations; make_pairsam = False, drop_readid = False, parsing_options: '--add-columns mapq --walks-policy mask', max_mismatch_bp = 1. Balanced multi-resolution cool (mcool) files were outputted with the following bin sizes: 10000000, 5000000, 2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 100.
The data was filtered using the mapq score of 30 to 100. The 15U and 20U Micro-C pairs files for each cell type were merged using pairtools merge (https://github.com/open2c/pairtools).
Assembly: mm9
Supplementary files format and content: .mcool files: format for high resolution genomic interaction matrices.

source_name: mouse embryonic fibroblasts

extract_protocol:
MEFs were cross-linked with 1% formaldehyde, chromatin digested with 15U or 20U MNase, and the fragmented DNA was ligated with T4 DNA ligase. Di-nucleosome sized DNA was excised from 1.5% low melting agaorse gel and purified using Zymoclean Gel recovery DNA kit .
Dynabeads™ MyOne™ Streptavidin C1 beads (Invitrogen #65001) were prepared depending on the amount of DNA present in Micro-C sample relative to the binding capacity of beads as specified by the manufacturer. The beads were then suspended 35µl 10mM Tris-HCl pH8.5, 3.5µl End Prep Reaction Buffer and DNA libraries were prepared using NEBNext Ultra II DNA library prep kit.

treatment_protocol: MEFs were infected with lentiviruses to over express the linker histon  H1 (H1OE), or knockdown H1 expression (H1KD).

value: MEFs infected with shRNA lentivirus to knock down linker histone H1 expression, 15U MNase Micro-C


title: 20U Mnase MicroC, MEF-H1KD

description: MEFs overexpressing linker histone H1

value: MEFs infected with shRNA lentivirus to knock down linker histone H1 expression, 20U MNase Micro-C


title: L313


title: L320


title: MEF, empty vector control, ATAC-seq, rep_3


title: L319


title: Cortex, 19-month old, Gde2KO3


title: L318


title: 20U Mnase MicroC, MEF-H1OE

description: MEFs overexpressing linker histone H1

value: MEFs infected with dox-inducible lentivirus to over express inker histone H1, 20U MNase Micro-C


title: L312

value: PFTa


title: 15U Mnase MicroC, MEF-H1OE

description: MEFs overexpressing linker histone H1

value: MEFs infected with dox-inducible lentivirus to over express inker histone H1, 15U MNase Micro-C


title: Cortex, 19-month old, Gde2KO2


title: L317


title: Otof_hom_Rep2

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

data_processing:
NextFlow RNA pipeline
Salmon used for counting transcripts.
DeSeq2 used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: Otof_salmon_genecounts.tsv; raw gene counts from salmon used as input for DESEQ2
Supplementary files format and content: DEGsOtofKOP7.xlsx; differentially expressed genes from Deseq2

source_name: cochlea

extract_protocol:
cochlear tissues were homogenized with Qiagen's RLT buffer using a plastic homogenizer and RNA eas extracted using the Qiagen microRNAeasy column. Samples were tested for a RIN values >9 before sequencing.
mRNA was purfied using poly-T olgio attached magentic beads. After fragmentation, the frist strand cDNA was synthesized usign random hexamer primers, followed by second stand cDNA synthesis using dTTP primers. End repari, A-tailing was reported, before adapter ligation and size seldction.

value: cochlea

value: Homozygous


title: Cortex, 4-month old, Gde2KO2


title: L316


title: MEF, ATAC-seq, rep_2


title: Cortex, 19-month old, WT3

value: WT


title: Cortex, 4-month old, WT3


title: Cortex, 19-month old, WT2


title: MEF, ATAC-seq, rep_1


title: MEF, empty vector control, ATAC-seq, rep_2


title: Otof_het_Rep1

value: Heterozygous


title: Cortex, 19-month old, WT1


title: Cortex, 4-month old, WT1


title: Cortex, 4-month old, Gde2KO3


title: L311


title: L303


title: L306


title: Otof_hom_Rep1


title: Otof_het_Rep2


title: L305


title: L304


title: Infected lung 4

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: GRCm38
Supplementary files format and content: Tab delimited file (txt) for raw hit counts

source_name: Lung

extract_protocol:
RNA was extracted from purified cells in Direct-Zol (Zymo) using a direct-zol micro RNA kit (Zymo) according to the manufacturers instructions
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Lung

value: Monocytes

value: Wild type

value: Staphylococcus aureus infection


title: Infected lung 2


title: Cortex, 4-month old, WT2


title: L296


title: mARF10_Mock_rep3

city: Wuhan

first: Limin

last: Pi

state: Hubei province

address: No.299 Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
Reads quality control was performed by Trimmomatic (v0.39) on raw reads to obtain clean reads. The criteria were as follows: adapter removing, low-quality reads removing (including reads with more than 10% of base 'N' or more than 20% of base sequencing quality less than 20), and only paired reads keeping.
Clean reads were mapped to reference genome of the Arabidopsis thaliana by histat2 (v2.2.0), the version of genome sequence file and gene annotation file was TAIR10.
FPKM was calculated by unique  mapped  reads  with  cufflink  (v2.2.1)  with  ‘--library-type  fr-unstranded’ parameter.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Arabidopsis thaliana

source_name: root tip

growth_protocol: Seeds were sterilized in 10% sodium hypochlorite and grown vertically half-strength on Murashige and Skoog (MS) medium containing 1% Agar and 1% sucrose under long-day condition (16 h light/8 h dark period, 22°C)

extract_protocol:
Root meristems at 5 dpg of approximately 500 µm were dissected under a stereomicroscope. For each genotype, 20 meristems were collected and subjected to RNA extraction using the RNeasy Plant Mini  Kit (Qiagen).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: root tip

value: mock


title: heart, COX8-AGO2, 1

first: zhan

last: jiabing

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: Mus musculus (Ensembl_release109)

source_name: Heart

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.

value: Heart


title: L299

value: PBMCs


title: miR160 OE_Mock_rep3


title: Cortex, 4-month old, Gde2KO1

value: brain, cortex


title: miR160 OE_Mock_rep2


title: mARF10_Mock_rep1


title: heart, GFP, 1


title: L300


title: L294


title: miR160 OE_Mock_rep1


title: Naïve bone marrow 3

source_name: Bone marrow

value: Bone marrow

value: control naive


title: arf10 arf16_Mock_rep3


title: L297


title: L293

value: PFTa


title: Infected lung 3


title: L298


title: L292


title: Naïve bone marrow 2


title: Naïve bone marrow 1


title: Infected lung 1


title: mARF10_Mock_rep2


title: L290


title: col_Mock_rep3


title: 20U Mnase MicroC, mTSCs

data_processing:
Micro-C libraries were aligned to mm9 and processed using the Nextflow  pipeline distiller-nf.
genome build: mm9
The aligned Micro-C data were processed using the Nextflow (https://www.nextflow.io/) pipeline distiller-nf (https://github.com/open2c/distiller-nf) using following configurations; make_pairsam = False, drop_readid = False, parsing_options: '--add-columns mapq --walks-policy mask', max_mismatch_bp = 1. Balanced multi-resolution cool (mcool) files were outputted with the following bin sizes: 10000000, 5000000, 2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000, 2000, 1000, 500, 100. The data was filtered using the mapq score of 30 to 100. The 15U and 20U Micro-C pairs files for each cell type were merged using pairtools merge (https://github.com/open2c/pairtools).
Library strategy: Micro-C

source_name: mTSCs

growth_protocol: Mouse TSCs were maintained on γ-irradiated feeder MEFs on 0.2% gelatin in TS Reprogramming Medium (RPMI-1640 (Thermo #21875034), 20% FCS, 0.1mM βME, 1X Non-Essential Amino Acids, Penn (100U/mL) Strep (100µg/mL), 25ng/ml hFGF4 (R&D #235-F4-025), 1µg/ml Heparin (Sigma #H3149)). TSCs  were then maintained on 0.2% gelatin in 70:30 TSC media (70% MEF conditioned TSC Reprogramming Medium, 30% fresh TSC Reprogramming Medium, freshly supplemented with 25 ng/ml hFGF4 and 1µg/ml Heparin). MEF conditioned TSC Reprogramming medium was prepared by culturing 6 x 106 γ-irradiated MEFs (R&D# PSC0001) in 30ml TSC Reprogramming media in absence of hFGF4 and Heparin for 72 h.

value: mTSCs

value: Mouse Trophoblast Stem cells

tag: chip antibody

value: MNase digested and ligated DNA

value: final reprogramming


title: L295


title: col_Mock_rep2

value: WT


title: arf10 arf16_Mock_rep2


title: Naïve bone marrow 4


title: 20U Mnase MicroC, mESCs

source_name: mESCs

growth_protocol: Mouse ESCs were grown on 0.2% gelatine and maintained in ESC Medium (GMEM, 10% FCS, 1mM L-glutamine, 0.1mM βME, 1X Non-Essential Amino Acids, 100U/ml Leukaemia Inhibitory Factor (LIF)

value: mESCs

value: Mouse Embryonic Stem cells


title: L289


title: col_Mock_rep1


title: 15U Mnase MicroC, mTSCs

extract_protocol: Mouse TSCs were maintained on γ-irradiated feeder MEFs on 0.2% gelatin in TS Reprogramming Medium (RPMI-1640 (Thermo #21875034), 20% FCS, 0.1mM βME, 1X Non-Essential Amino Acids, Penn (100U/mL) Strep (100µg/mL), 25ng/ml hFGF4 (R&D #235-F4-025), 1µg/ml Heparin (Sigma #H3149)). TSCs  were then maintained on 0.2% gelatin in 70:30 TSC media (70% MEF conditioned TSC Reprogramming Medium, 30% fresh TSC Reprogramming Medium, freshly supplemented with 25 ng/ml hFGF4 and 1µg/ml Heparin). MEF conditioned TSC Reprogramming medium was prepared by culturing 6 x 106 γ-irradiated MEFs (R&D# PSC0001) in 30ml TSC Reprogramming media in absence of hFGF4 and Heparin for 72 h.


title: arf10 arf16_Mock_rep1


title: L287


title: 20U Mnase MicroC, MEFs

source_name: MEFs

extract_protocol: Early passage (passage 1) mouse embryonic fibroblasts (MEFs) were cultured for 48hr in MEF medium (GMEM medium supplemented with 10% FCS, 1 mM sodium pyruvate, 1 mM glutamine, and 5.7 ml MEM 100X Non-Essential Amino Acids Solution, 50 M 2-mercaptoethanol (Gibco, Thermo Fisher Scientific) at 37C and 5% CO2.

value: MEFs

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage from 129 mouse line

value: Non-reprogrammed


title: 15U Mnase MicroC, mESCs

extract_protocol: Mouse ESCs were grown on 0.2% gelatine and maintained in ESC Medium (GMEM, 10% FCS, 1mM L-glutamine, 0.1mM βME, 1X Non-Essential Amino Acids, 100U/ml Leukaemia Inhibitory Factor (LIF)


title: 15U Mnase MicroC, MEFs


title: L288

extract_protocol:
cells were resuspended in DNA Quick Extraction solution (Lucigen) to lyse the cells and extract genomic DNA. The cell lysate was incubated at 65 °C for 5 min, then 95 °C for 5 min, and stored at −20 °C.
A 25 µl PCR-reaction contained 10 µl of genomic DNA, 0.5 µl 10 µM primer forward, 0.5 µl 10 µM primer reverse,  12.5 µl 2x GoTaq Long PCR Master Mix (Promega) and 1.5 µl H2O. The thermocycler setting consisted of one step at 95 °C for 1 min; followed by 18 cycles at 98°C for  10 s, 65°C for 15 s and 72°C for 15 s (wherein the annealing temperature was decreased by 0.5 °C per cycle); followed by 15 cycles at 98°C for 10 s, 58°C for 15 s and 72°C for 15 s; with one final step at 72°C for 5 min. The PCR products were cleaned up using AMPure beads according to the manufacturer's recommendations (Beckmann Coulter) and eluted in 50 µl 10 mM Tris. For barcoding, 2 µl of the purified DNA were added to 10 µl of 2x GoTaq Long PCR Master Mix, 2 µl of Nextera XT index 1 (i7) primer, 2 µl of Nextera XT index 2 (i5) primer (Illumina) and 4 µl of H2O. The PCR reactions were heated up to 95 °C for 3 min, followed by 8 cycles of 95°C for  30 s, 55°C for 30 s and 72°C for 30 s and a further elongation step for 5 min at 72°C. The second PCR products were again purified with AMPure beads and eluted in  27.5 µl 10 mM Tris. Cleaned-up PCR products were quantified using the SpectraMax Quant AccuBlue HighRange dsDNA Kit (Molecular Devices) on the SpectraMax 3x instrument (Molecular Devices). Equal amounts of DNA/sample were pooled and sequenced on an Illumina MiSeq instrument (Illumina) with a MiSeq Reagent Nano Kit v2 (500-cycles) (Illumina) according to the manufacturer’s recommendations.


title: 64U MNase, mTSCs

data_processing:
MNase pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters. Nucleosome and nucleosome dyad positions were called using the DANPOS2 function dpos with a 1% false discovery rate (FDR), paired-end settings and bin size of 1bp to ensure dyad position accuracy. The smoothened .wig file of MNase signal from DANPOS2 was converted to bigwig using wigToBigWig.
genome build: mm9
processed data file: The aligned MNase-seq data were smoothened using DANPOS2. The  smoothened MNase .wig file was  converted to bigwig using wigToBigWig

extract_protocol: MNase-seq experiments were carried out as described in Mieczkowski, et al. Nat Commun. (2016). doi: 10.1038/ncomms11485. And Iwafuchi-Doi, et al. Mol Cell. (2016). doi: 10.1016/j.molcel.2016.03.001.

value: MNase digested DNA


title: GFP_NRCM D14

first: Hee Cheol

last: Cho

state: MD

address: 600 N Wolfe St. Blalock 1257

institute: Johns Hopkins University

description: Adc-GFP treated NRCM for 14 days

data_processing:
The scRNA-seq data were analyzed with Partek Flow (Partek Inc., USA). Flow version:10.0.21.0621
FASTQ sequencing files were aligned to the custom rattus norvegicus reference genome (Rnor_6.0) with transgene (hTBX18，EGFP and ZsGFP) using STAR-2.7.8a aligner
The transcript abundance was estimated using the Partek E/M algorithm based on Ensembl release 104 transcript model with default settings.
Genome_build: The custom rattus norvegicus reference genome (Rnor_6.0) with hTBX18, GFP, ZsGFP
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Ventricle

extract_protocol:
Attached NRVC monolayers were digested with 0.25% trypsin (Cat# LS003707, Corning, NY) for 5 min at 37 °C, and filtered through a 100-μm cell strainer (Fischer Scientific, Waltham, MA) to generate a single-cell suspension. Single cells were resuspended to a concentration of 700-2,000 cells per microliter for further barcoding and RNA library.
RNA libraries were prepared using the Chromium Next GEM Single Cell 3' GEM kit, v3.1 (10X Genomics Inc., Pleasanton, CA) with a targeted cell recovery of 4,000-10,000 cells per reaction. Quality control of cDNA and scRNA-seq libraries were performed using the Bioanalyzer High Sensitivity kit (Agilent Technologies Inc., CA). Libraries were sequenced using Novaseq 6000 (Illumina Inc., CA) with a minimum depth of 50,000–65,000 read pairs per cell

value: Sprague dawley

value: neonatal ventricular cells (including myocytes and non-myocytes)

value: wild type

value: primary cells

value: Adeno-GFP for 14 days


title: TBX18_NRCM+A8301 D14

description: Adc-TBX18 treated NRCM plus A83-01 for 14 days

value: Adeno-TBX18 with A83-01 (0.2uM) for 3days


title: L152

value: PBMCs

value: PFTu


title: TBX18_NRCM D14

description: Adc-TBX18 treated NRCM for 14 days

value: Adeno-TBX18 for 14 days


title: TBX18_NRCM D3

description: Adc-TBX18 treated NRCM for 3 days

value: Adeno-TBX18 for 3 days


title: L291


title: L274


title: L151


title: GFP_NRCM D3

description: Adc-GFP treated NRCM for 3 days

value: Adeno-GFP for 3 days


title: 16U MNase, mTSCs

value: mTSCs

value: Mouse Trophoblast Stem cells

value: final reprogramming


title: 1U MNase, mTSCs


title: 4U MNase, mTSCs


title: LHLK, 24-hr fed or starved, batch 4

city: Stony Brook

first: Meng-Fu

middle: Maxwell

last: Shih

state: NY

address: 100 Nicolls Road

department: Anesthesiology

institute: Stony Brook University

description: including column names in the processed data files: lk4_028,lk4_098,lk4_099,lk4_102,lk4_103,lk4_104,lk4_105,lk4_107,lk4_108,lk4_110,lk4_111,lk4_112,lk4_113,lk4_114,lk4_115,lk4_116,lk4_117,lk4_118,lk4_119,lk4_121,lk4_122,lk4_123

data_processing:
Raw read files were generated by Illumina HiSeq 2500 sequencer system
umi_tools extract to extract UMI sequence for each read pair and add it into read name
A perl code provided by Simon Andrews to merge Read 1 and Read 2
fastx_barcode_splitter.pl in the FASTX-Toolkit was used to split or demultiplex single cell reads into individual files based on barcode sequences, with 1 mismatch allowance
fastx_trimmer in the FASTX-Toolkit was used to trim non-transcript sequence off the merged reads
fastx_masker in the FASTX-Toolkit was used to mask base calls that have a quality score lower than 10
STAR was used for alignment with default configuration
htseq-count was used for counting mapped read numbers for each annotated genes and to output as BAM files
samtools view, sort, and index were used for file format preparation for downstream deduplication.
umi_tools count was used to deduplicate the read count numbers with 'directional' method based on the UMI sequences in the read name, and to output count matrix for each single LHLK neuron
custom R code was used to convert the count matrix (SupplTab2_Patch-seq_41LHLK_count.csv) into normalized TPM matrix (SupplTab3_Patch-seq_41LHLK_TPM.csv)
Assembly: dm6
Supplementary files format and content: SupplTab2_Patch-seq_41LHLK_count.csv is a comma-separated value file that includes deduplicated raw counts for each LHLK neuron that has passed QC
Supplementary files format and content: SupplTab3_Patch-seq_41LHLK_TPM.csv  is a comma-separated value file that includes normalized Transcript Per Million (Deduplicated) Mapped Reads (TPM) for each LHLK neuron that has passed QC

organism: Drosophila melanogaster

source_name: LHLK

growth_protocol: Flies were grown and maintained on standard Drosophila food media (Bloomington Recipe, Genesee Scientific, San Diego, California) in incubators (Powers Scientific, Warminster, Pennsylvania) at 25°C on a 12:12 LD cycle with humidity set to 55–65%.

extract_protocol:
In brief, after tethering cold-anesthetized fly on a custom fly stage and immersing the fly head in isotonic PBS, microdissection was conducted to remove the posterior dorsal lateral head cuticle to allow access to the LHLK neurons. A custom rig equipped with micromanipulator and infra-red and fluorescent DIC and glass electrodes were used to harvest the individual LHLK neurons from both sides of the animal’s brain. After harvesting each LHLK neuron, the tip of electrode was broken into a microcentrifuge tube prefilled with PBS with RNase inhibitor. The tube was briefly mixed, flash frozen in liquid nitrogen, and stored at –80 ℃ before library construction. Sampling between starvation and control groups was performed in an alternating manner.
CEL-Seq2 protocol. In brief, 18 to 28 harvested LHLK neurons were processed in parallel for individual library constructions. Single-cell RT was conducted with primers that contain sequences of Illumina RNA 5’ adaptor (RA5), hexamer UMI, single-cell barcode, and poly-T ending with V (not T), followed by second-strand synthesis. Then, all the samples were pooled together for in-vitro transcription-based amplification. A second round of RT was conducted with a primer that contain 3’-end common sequence of Illumina RNA PCR Index Primer sets and random hexamer, followed by 11-cycles of PCR. After 2 rounds of bead cleanup, the libraries were quantified by Qubit, size-profiled by Bioanalyzer, and ready for sequencing

treatment_protocol: The starvation group in vials with agar gel or the control group in vials with regular fly food; we housed approximately 20 sex-mixed flies. Vials were placed on their side in the temperature- and humidity-controlled incubator.

value: female

value: LHLK

value: mixed samples (fed, starved)


title: L141

data_processing:
Screening for deletion using CRISPResso2 (V2.2.7)
Reads for each deletion were normalised and displayed in a cumulative way
Assembly: hg38
Supplementary files format and content: .txt file with the range of deletions
Library strategy: Amplicon-Sequencing


title: 64U MNase, mESCs

value: mESCs

value: Mouse Embryonic Stem cells

value: MNase digested DNA


title: LHLK, 24-hr fed or starved, batch 1

description: including column names in the processed data files: lk1_043,lk1_044,lk1_046,lk1_049,lk1_050,lk1_052,lk1_053,lk1_054,lk1_055,lk1_057,lk1_058


title: LHLK, 24-hr fed or starved, batch 3

description: including column names in the processed data files: lk3_078,lk3_086,lk3_088,lk3_089,lk3_092,lk3_096,lk3_100,lk3_101


title: L142


title: 16U MNase, mESCs


title: L139


title: L269


title: 4U MNase, mESCs


title: L140


title: L099


title: 64U MNase, MEFs

value: MEFs

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage from 129 mouse line

value: Non-reprogrammed


title: L100

value: PBMCs


title: 16U MNase, MEFs


title: L101


title: muscle, non_radiated, left, 2015-5182

city: Salt Lake City

first: Sujee

last: Jeyapalina

state: Utah

address: 500 Foothill Dr

institute: Department of Veteran Affairs

data_processing:
Aligned to reference genome GRCh38 using STAR.
Feature counts calculated using featureCounts Subread.
Normalization and differential expression performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: raw_counts.txt provide the count matrix generated from featureCounts for all samples.

source_name: muscle

extract_protocol:
Trizol
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold

value: muscle

tag: side

value: left

tag: collection alias


title: fibrous capsule, radiated, right, 2015-5708

source_name: fibrous capsule

value: fibrous capsule

value: radiated

value: right


title: skin, radiated, right, 2015-5859

source_name: skin

value: skin


title: skin, non_radiated, left, 2015-5708


title: 4U MNase, MEFs


title: L098


title: muscle, radiated, right, 2015-5859


title: Esrrb-ChIP-seq, miTSCs

data_processing:
The pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters. Duplicated reads were then removed using MarkDuplicates from the Picard toolkit. Reads mapping to the backlisted regions as determined by Encyclopaedia of DNA Elements (ENCODE) were discarded. The sequencing coverage and the insert size distribution were measured from the resulting bam files using Qualimap (version 2.2.1). The peaks of TFs showing significant enrichment over input DNA were called using MACS2 (version 2.1.1.20160309), and a fragment size of 200 bp and were controlled to a q-value (minimum FDR) cut-off of 0.01. The peaks that overlapped with the ENCODE blacklist were removed.
genome build: mm9
processed data file: The aligned ChIP-seq reads (bam files) were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters. BAM files from replicates were merged before normalized for coverage

source_name: miTSCs-BYKE

growth_protocol: Mouse iTSCs were maintained on γ-irradiated feeder MEFs on 0.2% gelatin in TS Reprogramming Medium (RPMI-1640 (Thermo #21875034), 20% FCS, 0.1mM βME, 1X Non-Essential Amino Acids, Penn (100U/mL) Strep (100µg/mL), 25ng/ml hFGF4 (R&D #235-F4-025), 1µg/ml Heparin (Sigma #H3149)). iTSCs  were then maintained on 0.2% gelatin in 70:30 TSC media (70% MEF conditioned TSC Reprogramming Medium, 30% fresh TSC Reprogramming Medium, freshly supplemented with 25 ng/ml hFGF4 and 1µg/ml Heparin). MEF conditioned TSC Reprogramming medium was prepared by culturing 6 x 106 γ-irradiated MEFs (R&D# PSC0001) in 30ml TSC Reprogramming media in absence of hFGF4 and Heparin for 72 h.

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072756

value: miTSCs-BYKE

value: Mouse induced Trophoblast Stem cells  with Nanog-GFP reporter

value: BYKE

value: final reprogramming


title: L090


title: L085


title: 1U MNase, MEFs


title: L091


title: fibrous capsule, radiated, right, 2015-5859


title: fibrous capsule, non_radiated, left, 2015-5708


title: Input-ChIP-seq, BS9G4M-48h, biol rep 2

description: Input-ChIP-seq_BS9G4M48h.SeqDepthNorm.bw

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072758

treatment_protocol: MEFs were seeded onto 15-cm dishes and cultured for 24hr in MEF medium before being infected with Tet-on-TFs  and rtTA2M2 lentiviruses at a multiplicity of infection (M.O.I) of 5 for each virus. TF overexpression was induced by treating infected cells with 1 g/mL Dox for 48hr.

value: Input DNA control

value: early reprogramming


title: muscle, non_radiated, left, 2015-5859


title: L084


title: 1U MNase, mESCs

value: mESCs

value: Mouse Embryonic Stem cells

value: MNase digested DNA


title: fibrous capsule, non_radiated, left, 2015-5859


title: muscle, non_radiated, right, 2015-5293


title: Input-ChIP-seq, BS9G4M-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072757

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage from 129 mouse line


title: L083

value: PBMCs


title: Sox9-ChIP-seq, BS9G4M-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072754

value: Sox9 (Millipore, AB5535)


title: Sox9-ChIP-seq-BS9G4M48h_rep1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072753


title: skin, radiated, left, 2015-5293

value: left


title: Ko-3

city: Research Unit for Molecular Medicine (MMF)

first: Peter

last: Bross

state: Region Midt

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University and Aarhus University Hospital

data_processing:
Data was obtained from BGI in fastq file format. Initial quality control of the fastq files was conducted using FastQC (Babraham Bioinformatics). Adaptor removal and trimming of low-quality ends were performed using Trim Galore with default settings (Babraham Bioinformatics). Gene expression was quantified using Salmon against decoy-aware reference transcriptomes (Danio rerio, GRCz11). Transcript abundances were calculated and summarized at the gene level with tximeta. Differential expression analysis was performed using DESeq2 , applying a false discovery rate (FDR) threshold of less than 0.05.
Assembly: GRCz11
Supplementary files format and content: Comma-delimited files contain raw data for each sample

source_name: embryo

growth_protocol: Adult hspd1+/- zebrafish lines were housed and maintained at 28°C with 14/10 hours light/dark cycle. The F4 generation of the zebrafish hspd1+/- knockout line was in-crossed and obtained embryos were maintained at 28.5°C in E3 buffer (5 mm NaCl, 0.17 mm KCl, 0.33 mm CaCl2, 0.33 mm MgSO4, 10−5% methylene blue, 2 mM HEPES, pH 7.4) with daily replacements until 5 dpf.

extract_protocol:
The 5 dpf larvae were anesthetized with 150 mg/L tricaine in groups of four at a time. The tip of the caudal fin of the anesthetized larvae was then removed using a hypodermic needle. The tail was transferred to a 96-well plate with 100% methanol-filled wells for genotyping. The larvae bodies were covered with 25 µL TRIzol (Invitrogen; #15596-018) and stored at -80°C until RNA extraction. According to the obtained genotyping results, bodies of hspd1+/+ and hspd1-/- larvae were pooled in groups of 5 larvae, and this process was repeated for 3 mating sets, resulting in 6 samples in total. Pooled samples were homogenized with a motorized pellet pestle (Kimble; #Z359971). RNA isolation was performed using TRIzol, including DNase treatment with DNA-free Kit (Ambion, AM1906) according to the manufacturer’s instructions. Total RNA concentrations were determined with Synergy H1 plate reader equipped with Take3 Plate (BioTek, Agilent). Quality control analysis was performed with an automated 4200 TapeStation System (Agilent, G2991AA), and RNA integrity number (RIN) values were determined by RNA ScreenTape Assay for 4200 TapeStation System according to the manufacturer’s instructions. RIN values were above 8.3 for all samples. RNA sequencing service was performed by BGI Copenhagen by a non-stranded and polyA-selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.immediately snap-frozen in an empty 96-well plate (Biorad; #12001925) on dry ice and stored at -80°C until sample preparation.
Library preparation and RNA sequencing service was performed by BGI Copenhagen by a non-stranded and polyA-selected RNA library preparation and a consequent PE100 sequencing on DNBSEQ.

value: embryo

value: 5 dpf

value: hspd1 knockout


title: muscle, radiated, left, 2015-5293

value: muscle

value: radiated


title: Myc-ChIP-seq, BS9G4M-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072755


title: skin, non_radiated, left, 2015-5859

value: skin


title: fibrous capsule, non_radiated, right, 2015-5293

value: fibrous capsule

value: right


title: control-3

value: control


title: Myc-ChIP-seq, BS9G4M-48h, biol rep 2

value: early reprogramming


title: control-1


title: skin, non_radiated, right, 2015-5293


title: skin, radiated, right, 2015-5182


title: Esrrb-ChIP-seq, mESCs

value: Mouse Embryonic Stem cells with Oct4-GFP reporter

value: final reprogramming


title: Gata4-ChIP-seq, BS9G4M-48h, biol rep 2

description: Gata4-ChIP-seq_BS9G4M48h.SeqDepthNorm.bw

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072750

value: Gata4 (Santa-Cruz, sc-1237-X)


title: Brn2-ChIP-seq, BS9G4M-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072752

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage from 129 mouse line

value: Brn2 (Santa-Cruz, sc-6029-X)


title: fibrous capsule, radiated, left, 2015-5293


title: control-2


title: aa3mprA mutant_rep2

city: Busan 46241, Republic of Korea

first: Yuna

last: Oh

address: Busandaehakro63bun-gil, 2

department: Department of Integrated Biological Science

country: South Korea

institute: Pusan national university

data_processing:
The quality of the obtained data was checked by determining the phred quality score using FastQC v0.11.7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.38, then mapped to the whole genome of M. smegmatis using bowtie v1.1.2 with default setting.
Mapped reads per annotated gene were counted by Htseq v0.10.0.
Counted values were nomalized in the FPKM method.
Assembly: Mycobacterium smegmatis MC2 155 (GCF_000015005.1_ASM1500v1)
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

organism: Mycolicibacterium smegmatis

growth_protocol: The M. smegmatis strains were grown aerobically in Middlebrook 7H9 medium supplemented with 0.2% glucose and 0.02% Tween 80 (vol/vol) on a gyratory shaker (200 rpm) at 37°C.

extract_protocol:
The stains were grown until an optical density at 600 nm reached 0.45 to 0.5. Cells were harvested by centrifugation at 4°C with 3500×g for 3 min. The cell pellets were resuspended with 1 ml TRIzol (Invitrogen). Procedures of total RNA extract from the cell pellets were performed using TRIZol purchased from Invitrogen and followed the instructions provided to users.
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape (Agilent). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction. A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).

value: bacterial cell


title: Brn2-ChIP-seq, BS9G4M-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072751


title: Ko-2


title: fibrous capsule, radiated, right, 2015-5182


title: L082

value: PBMCs


title: skin, non_radiated, left, 2015-5182

value: left


title: muscle, radiated, right, 2015-5182


title: Input-ChIP-seq, GETMR-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072748

value: Input DNA control


title: aa3mprA mutant_rep1


title: Input-ChIP-seq, GETMR-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072747


title: Gata4-ChIP-seq, BS9G4M-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072749


title: aa3rel mutant_rep1


title: Ko-1

value: embryo

value: 5 dpf

value: hspd1 knockout


title: muscle, radiated, right, 2015-5411

value: muscle

value: radiated


title: fibrous capsule, non_radiated, left, 2015-5182

value: fibrous capsule


title: aa3rel mutant_rep2


title: skin, radiated, right, 2015-5411

value: skin

value: right


title: Myc-ChIP-seq, GETMR-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072744

value: early reprogramming


title: aa3 mutant_rep2


title: RESUB-C3

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
The gene counts were normalized by rlog transformation and analyzed by the DeSeq2 pipeline. The analyzed DeSeq2 results were uploaded on the web-based application called iPathway Guide and significantly upregulated and downregulated genes and pathways were identified. The log2fold change threshold was >0.6 and the p-value threshold was <0.05 was applied.
Assembly: mm10
Supplementary files format and content: tab-delimited text files log read counts values for each Sample

organism: Mus

extract_protocol:
Total RNA extraction was done following Qiagen’s RNA easy mini plus kit. RNA quality, as assessed by RIN value >8.0 was confirmed by Agilent Bioanalyzer and further used for RNA library preparation and bulk RNA sequencing.
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: C57 BL/6 and C3HeB/FeJ mice, aged between 6-8 weeks were infected with ~100CFU of Mycobacterium tuberculosis HN878 for 28 days. At Day 29 post infection, mouse lung neutrophils were sorted by Magnet Associated Cell Sorting (MACS) using Biolegend Neutrophil Isolation kit according to the manufacturer’s instructions.

value: Lung

value: Neutrophils

tag: agent

value: Mycobacterium tuberculosis HN878


title: aa3 mutant_rep1


title: skin, non_radiated, left, 2015-5411

extract_protocol:
Trizol
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold


title: RESUB-C1


title: RESUB-C2


title: fibrous capsule, non_radiated, left, 2015-5411


title: Eomes-ChIP-seq, GETMR-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072740

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage from 129 mouse line

value: Eomes (Abcam, ab23345)


title: RESUB-B2


title: muscle, non_radiated, right, 2015-5154


title: Tfap2c-ChIP-seq, GETMR-48h, biol rep 1

description: Tfap2c-ChIP-seq_GETMR48h.SeqDepthNorm.bw

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072741

value: Tfap2c (R&D, AF5059)


title: Eomes-ChIP-seq, GETMR-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072739


title: Tfap2c-ChIP-seq, GETMR-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072742


title: muscle, non_radiated, left, 2015-5411

value: left


title: Esrrb-ChIP-seq, GETMR-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072746


title: Esrrb-ChIP-seq, GETMR-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072745


title: RESUB-B3


title: Gata3-ChIP-seq, GETMR-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072737


title: Gata3-ChIP-seq, GETMR-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072738


title: skin, non_radiated, right, 2015-5154


title: HEK293T_DNMT1_KO_WGBS_rep3

city: Guangzhou

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

institute: South China Normal University

data_processing:
The WGBS libraries were sequenced using NovaSeq 6000 analyzer with paired end reads of 150 bp read length (PE150) according to the manufacturer’s instructions. Low quality bases and adapter sequences were trimmed by using trim_galore. The cleaned reads were mapped back to hg38 genome using BSMAP software version 2.90. The parameter settings used was “-n 0 -v 0.08 -g 1 -p 48”. Methylation ratios were extracted from BSMAP output (SAM) using a Python script (methratio.py) which is distributed with the BSMAP package. In brief, The methylation level was calculated based on the methylated cytosine (mC) percentage in the whole genome as site methylation level = 100× (number of sequences with methylated cytosines (mC)/total number of valid sequences).
Assembly: hg38
Supplementary files format and content: The methylation level  based on the methylated cytosine (mC)

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
DNA was isolated using the Cell Culture DNA Midi Kit from QIAGEN (Qiagen, 13343). Prior to library construction, 1µg sample genome DNA mixed with unmethylated lambda DNA was fragmented using a Bioruptor system to a mean size of approximately 250bp
After fragmentation, the purified randomly fragmented DNA was subsequently treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate the ends. The blunt DNA fragments were subsequently 3’ adenylated using Klenow Fragment (3’-5’ exo-) (Enzymatics, P7010-LC-L) and following with ligation to adaptors synthesized with 5’-methylcytosine instead of cytosine using T4 DNA Ligase. Then, the DNA was purified using QIAquick PCR purification kit (Qiagen, 28104). After that, ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO, D5005) was employed to convert unmethylated cytosine into uracil according to the instructions. Finally, the WGBS libraries were generated by PCR amplification using JumpStartTM Taq DNA Polymerase (Sigma, D4184-50UN) and purification using QIAquick PCR purification kit (Qiagen, 28104).

value: Human embryonic kidney


title: HEK293T_DNMT1_KO_WGBS_rep2


title: RESUB-B1


title: fibrous capsule, non_radiated, right, 2015-5154


title: fibrous capsule, radiated, right, 2015-5411


title: HEK293T_WT_WGBS_rep3

value: WT


title: Myc-ChIP-seq, GETMR-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072743


title: Input-ChIP-seq, GETM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072735

value: Input DNA control


title: muscle, radiated, left, 2015-5154


title: HEK293T_WT_WGBS_rep2


title: fibrous capsule, radiated, left, 2015-5154


title: Myc-ChIP-seq, GETM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072734


title: skin, radiated, right, 2015-5708


title: Myc-ChIP-seq, GETM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072733


title: muscle, radiated, right, 2015-5708


title: HEK293T_DNMT1_KO_BG4_rep3

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore-0.6.7, discarding reads left with < 20 bp
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.4.5.
The aligned reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per million, BPM) with the bamCoverage command from deepTools 3.3.0
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=1E-5
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed essentially as described by Kaiwei Liang et al. 2021, with minor modifications according the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).One hundred thousand cells were used for the CUT&Tag experiment, and cell counting was performed by using a Cellometer Mini (Nexcelom Bioscience, Boston, MA, USA). pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.
Libraries were prepared according to Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China)


title: Tfap2c-ChIP-seq, GETM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072731


title: Tfap2c-ChIP-seq, GETM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072732


title: HEK293T_WT_BG4_rep3


title: skin, radiated, left, 2015-5154

extract_protocol:
Trizol
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold


title: skin, non_radiated, right, 2015-5393


title: 293T_WT_ATAC_rep3

data_processing:
ATAC-seq reads were aligned to human genome hg38. The aligned reads were removed with Picard MarkDuplicates, Blacklisted regions were removed from the BAM file with bedtools intersect, and the deduplicated BAM files were normalized (Bins Per Million mapped reads, BPM) to generate bigwig file with the bamCoverage command from deepTools 3.3.0.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
ATAC-seq was performed as previously described (Li et al. 2021). Briefly, 5×104 cells were collected and washed with cold PBS and centrifuged at 500 g for 5 minutes. Then, the cells were lysed by 50 μl cold lysis buffer (Novoprotein, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% NP-40, 0.1% Tween-20, 1% Digitonin) and incubated on ice for 5 minutes. The cells were furthered added with 950 μl cold wash buffer (Novoprotein, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl, 0.1% Tween-20) and centrifuged at 500 g for 5 minutes
The pellet was resuspended with 40 μl tagmentation buffer (Novoprotein, N248, 0.3×pbs, 0.1% Tween-20, 0.01% Digitonin, 1×TD buffer, 1×pA-Tn5 transposome Mix) incubated at 37 ℃ for 30 min. The reaction was stopped by adding 10 μl stop buffer (Novoprotein, N248) at 55 ℃ for 5 min. The DNA was further purified with 100 μl Tagment DNA Extract Beads (Novoprotein, N245) and eluted with 37 μl Elution buffer. The purifyied DNA was amplified with 5×AmpliMix (Novoprotein, N248) using N501 and N701 index primer((Novoprotein, N239). The purified DNA libraries were size selected with NovoNGS® DNA Clean Beads (Novoprotein, N240)


title: muscle, non_radiated, right, 2015-5393


title: 293T_DNMT1_KO_ATAC_rep2


title: Eomes-ChIP-seq, GETM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072730


title: fibrous capsule, non_radiated, right, 2015-5393


title: skin, radiated, left, 2015-5393


title: Gata3-ChIP-seq, GETM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072727


title: muscle, radiated, left, 2015-5393


title: Input-ChIP-seq, OSKM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072726


title: Gata3-ChIP-seq, GETM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072728


title: 293T_WT_ATAC_rep2


title: fibrous capsule, radiated, left, 2015-5393


title: Input-ChIP-seq, OSKM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072725


title: IS-06-09254

city: Ann Arbor

first: Simpa

middle: S

last: Salami

state: MI

address: 1500 E Medical Center Dr

department: Urology

institute: University of Michigan

data_processing:
libraries were normalized using TMM method prior to downstream processing
Assembly: GRCh38.p1
Supplementary files format and content: tab delimited text file with raw counts for each sample
Supplementary files format and content: tab delimited text file with logCPM for each sample

source_name: Bone

extract_protocol:
1ug - 6μg of total RNA was used in a reverse transcription reaction, and the obtained cDNA was taken to a second-strand DNA synthesis as described
Briefly, following second-strand synthesis, we used the Sciclone G3 NGS workstation (Perkin Elmer) with the Kappa HT library preparation kit to produce the libraries

value: Bone


title: 293T_DNMT1_KO_ATAC_rep3


title: AA_HumanBrain_GBM_Tumor_935_10X_S37

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

description: GBM biopsy

data_processing:
Single nuclei: Raw base calls were demultiplexed to obtained sample specific FastQ files using mkfastq in default parameters (10x Genomics), and reads were aligned to GRCh38 genome assembly using the Cell Ranger pipeline (10x Genomics, Cellranger count v3.1.0) with default parameters (--include-introns was used for nuclei mapping)
Assembly: GRCh38
Supplementary files format and content: Single cell/nuclei: Cellranger count output matrices

source_name: GBM biopsy

extract_protocol:
Single nuclei RNAseq: Protocol based on published nuclei isolation protocol (Södersten et al., 2018).
Single nuclei RNAseq: Around 20 μg of -80 C-conserved tissue were thawed and dissociated in ice-cold lysis buffer (0.32M sucrose, 5 mM CaCl2, 3 mM MgAc, 0.1 mM Na2EDTA, 10 mM Tris-HCl pH 8.0, 1 mM DTT) using a 1 ml glass douncer (Wheaton). The homogenate was slowly and carefully layered in the centrifuge tubes on top of a sucrose layer (1.8 M sucrose, 3 mM MgAc, 10 mM Tris-HCl pH 8.0, 1 mM DTT) to create a gradient, and then centrifuged at 15500 rpm for 2 h 15 min. Following centrifugation, the supernatant was removed and the pellet softened for 10 minutes in 100 μl of nuclear storage buffer (15% sucrose, 10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2) prior resuspension in 300 μl of dilution buffer (10 mM Tris-HCl pH 7.2, 70 mM KCl, 2 mM MgCl2, Draq7 1:1000). The suspension was then filtered (70 μm cell strainer) and sorted via FACS (FACS Aria III, BD Biosciences) at 4° C with low flowrate, using a 100 μm nozzle (Pipette tips and Eppendorf tubes for transferring nuclei were pre-coated with 1% BSA).
Single nuclei RNAseq: 8500 nuclei were sorted for single-nuclei RNA-sequencing and then loaded onto the Chromium Next GEM Single Cell 3’ Kit (10x Genomics). Sequencing libraries samples were multiplexed and sequenced on a Novaseq machine using a 150-cycle kit using the recommended read length from 10x Genomics.

value: GBM biopsy

value: tumor sample

value: Brain, Glioblastoma


title: AA_HumanBrain_GBM_Tumor_592_10X_S17

description: GBM biopsy


title: AA_HumanBrain_GBM_Tumor_593_10X_S27

description: GBM biopsy


title: Myc-ChIP-seq, OSKM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072724


title: AA_HumanBrain_GBM_Tumor_499_10X_S6

description: GBM biopsy


title: muscle, non_radiated, left, 2015-5708

value: muscle


title: SU-15-8688

source_name: Adrenal

value: Adrenal


title: HuBrain_Tumor_no504_S11

description: GBM biopsy


title: Myc-ChIP-seq, OSKM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072723

value: early reprogramming


title: AA_HumanBrain_GBM_Tumor_483_10X

description: GBM biopsy


title: Klf4-ChIP-seq, OSKM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072722


title: IF-05-40491


title: HuBrain_Tumor_no487_S9

description: GBM biopsy


title: Input-ChIP-seq, GETM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072736


title: Sox2-ChIP-seq, OSKM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072719


title: HuBrain_Tumor_no473_S6

description: GBM biopsy


title: Eomes-ChIP-seq, GETM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072729


title: HuBrain_Tumor_no461_S5

description: GBM biopsy


title: IF-10-08610

source_name: Lung

value: Lung


title: Klf4-ChIP-seq, OSKM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072721


title: HuBrain_Tumor_no493_S10

description: GBM biopsy


title: IS-09-22020A

source_name: Soft tissue

value: Soft tissue


title: Sox2-ChIP-seq, OSKM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072720


title: IS-03-26079


title: HuBrain_Tumor_no459_S4

description: GBM biopsy


title: IS-05-51846


title: Oct4-ChIP-seq, OSKM-48h, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072718

value: Oct4 (Abcam, AB19857)


title: GU-06-35275


title: IS-03-21959


title: Sox2-ChIP-seq, miTSCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072716

value: miTSCs-BYKE

value: Mouse induced Trophoblast Stem cells  with three BYKE reporter

value: BYKE

value: final reprogramming


title: HuBrain_Tumor_no437_S3

description: GBM biopsy


title: Oct4-ChIP-seq, OSKM-48h, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072717

value: Mouse Embryonic fibroblasts isolated from embryos at E12.5 stage from 129 mouse line


title: IF-03-21898


title: Myc-ChIP-seq, miTSCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072714


title: IS-11-63453


title: HuBrain_Tumor_no476_S8

description: GBM biopsy


title: Sox2-ChIP-seq, miTSCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072715


title: IF-05-38205


title: HuBrain_Tumor_no435_S6

description: GBM biopsy


title: IS-02-21878

source_name: Lymph

value: Lymph


title: Myc-ChIP-seq, miTSCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072713


title: HuBrain_Tumor_no432_S5

description: GBM biopsy


title: IS-05-37079


title: HuBrain_Tumor_no440_S7

description: GBM biopsy


title: Tfap2c-ChIP-seq, miTSCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072711

value: Tfap2c (R&D, AF5059)


title: Tfap2c-ChIP-seq, miTSCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072712


title: GA-10-58544

source_name: Liver

extract_protocol:
1ug - 6μg of total RNA was used in a reverse transcription reaction, and the obtained cDNA was taken to a second-strand DNA synthesis as described
Briefly, following second-strand synthesis, we used the Sciclone G3 NGS workstation (Perkin Elmer) with the Kappa HT library preparation kit to produce the libraries

value: Liver


title: human medial pallium organoids, cell line: 8119-1

city: Stanford

first: Kevin

last: Kelley

address: 318 Campus Drive, W200

institute: Stanford University

description:
N4
10x 3' v3

data_processing:
For the 10x organoid samples, filtered count matrices were obtained using the CellRanger analysis soft-ware suite (version 7.1.0)
To ensure only high-quality cells were included for downstream anal-yses, an iterative filtering process was implemented. First, cells with less than the 5th percentile within the dataset of unique genes detected and with mitochondrial counts greater than 20% of the total counts were identified and removed. Subsequently, raw gene count matrices were normalized by regularized negative binomial regression using the sctrans-form function (vst.flavor=”v2”), which also identified the top 3,000 highly variable genes using default parameters. Dimensionality reduction using principal component analysis (PCA) on the top variable genes was performed and clusters of cells were identified in PCA space by shared nearest-neighbor graph construction and modularity detection implemented by the Find-Neighbors and FindClusters functions using a dataset dimension of 50 (dims=50 chosen based on visual inspection of elbow plot) with default parameters. We subsequently performed iterative rounds of clustering (resolution = 2) to identify and remove clusters of putative low-quality cells based on outlier low gene counts (median below the 10th percentile), outlier high fraction mitochondrial genes (median above the 95th percentile), outlier high fraction ribosomal genes (median above the 95th percentile), and/or high proportions of putative doublets identified by the DoubletFinder package (median DoubletFinder score above the 95th percentile). We iteratively removed low-quality clusters until no further clusters met the above thresh-olds. Following low quality cell removal, an additional round of filtering of putative stressed cells was performed using the Gruffi R package in addition to manual inspection and removal of clusters expressing markers associated with unfolded protein response (e.g. DDIT3, EIF2AK3).
Assembly: GRCh38, Ensemble release 98, for the human fetal scRNA-seq
Supplementary files format and content: csv or tsv files with feature (gene) and cell barcode information corresponding to row and column indices of gene count data for each sample
Supplementary files format and content: matrix exchange format for sparse matrices of gene count data for each sample (rows: genes; columns: cells)
Supplementary files format and content: Seurat object (.rds) of processed and filtered scRNA-seq data

source_name: hPS-derived medial pallium organoids

growth_protocol: Prior to neural differentiation, hiPS cells were cultured on vitronectin-coated plates (5 µg ml–1, Thermo Fisher Scientific, A14700) in Essential 8 medium with supplement (Thermo Fisher Scientific, A1517001). Cells were dissociated every 5 to 6 days with UltraPureTM 0.5 mM EDTA, pH 8.0 (Thermo Fisher Scientific, 15575) and passaged onto new plates. For the generation of 3D neural spheroids (day –1), hiPS cells were washed with PBS and incubated with Accutase (Innovative Cell Technologies, AT104) at 37C for 7 min. Cells were manually triturated with a P1000 into a single cell suspension and were passed through a 40 µM filter (FloMi). To generate spheroids, 3 x 106 hiPS cells were added to each AggreWell-800 well in Essential 8 medium supplemented with the ROCK inhibitor Y27632 (10 µM, Selleckchem, S1049), centrifuged at 100 g for 1 min, and then incubated at 37C in 5 % CO2. After 24 hours, spheroids of approximately 10,000 cells were formed. Spheroids were lifted from each microwell by pipetting medium in the well up and down with a cut P1000 pipet tip and were placed in Essential 6 medium (Thermo Fisher Scientific, A1516401) with the SMAD pathway inhibitors dorsomorphin (2.5 µM, Sigma-Aldrich, P5499) and SB-431542 (10 µM, R&D Systems, 1614). Molecules in the screen were added to the following basal media: from day 0 to day 6, spheres were cultured in Essential 6 medium and media was exchanged daily. From day 6 to day 21, spheres were cultured in neural medium consisting of Neurobasal™-A Medium (Thermo Fisher Scientific, 10888022), B-27™ Supplement, minus vitamin A (Thermo Fisher Scientific, 12587010), GlutaMAX™ Supplement (1:100, Thermo Fisher Scientific, 35050079), and Penicillin-Streptomycin (1:100, Thermo Fisher Scientific, 15070063) and media was exchanged daily. From day 21 onwards, spheres were cultured in Neurobasal™-A Medium (Thermo Fisher Scientific, 10888022), B-27™ Supplement, minus vitamin A (Thermo Fisher Scientific, 12587010), GlutaMAX™ Supplement (1:100, Thermo Fisher Scientific, 35050079), N-2 supplement (Life Technologies, 17502048) and Penicillin-Streptomycin (1:100, Thermo Fisher Scientific, 15070063) with BDNF (20 ng/ml; Peprotech), NT3 (20 ng/ml; Peprotech), (cAMP; 50 µM, Millipore Sigma, D0627), L-Ascorbic Acid 2-phosphate Trisodium Salt (AA; 200 µM, Wako, 323-44822) and media was exchanged every 2-3 days.

extract_protocol:
Three organoids from each condition were pooled at indicated day, incubated in 30 U/mL papain enzyme solution (Worthington Biochemical, LS003126) and 0.4% DNase (12,500 U/mL, Worthington Biochemical, LS2007) at 37 °C for 45 minutes. Organoids were triturated with a P1000 pipette and were resus-pended in FBS followed by trituration with a P200 pipette tip. Cells were resuspended in PBS with 0.4% DNase and filtered through a 70 μm Flowmi Cell Strainer (Bel-Art, H13680-0070). The samples were centrifuged at 200 x g for 3 minutes and were resuspended in Parse Cell Buffer containing BSA. Cells were then fixed using the Parse Biosciences Cell Fixation (Parse Biosci-ences, ECF2001) kit and stored at −80°C.
To target 7,000 cells after recovery, approximately 11,600 cells were loaded per lane on a Chromium Single Cell 3′chip (Chromium Next GEM Chip G Single Cell Kit, 10x Genomics, PN-1000127) and cDNA libraries were generated with the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000128), according to the manufacturer’s instructions. The library was sequenced using the Illumina NovaSeq S4 2 × 150 bp at Admera Health

treatment_protocol: Molecules used: EGF (R&D Systems, 236-EG), FGF2 (R&D Systems, 233-FB), IWP-2 (STEMCELL Technologies, 72124), RA (Sigma, R2625), 2.5 µM DAPT (STEMCELL Technologies, 72082), brain-derived neurotrophic factor (BDNF; 20ng ml-1, PeproTech, 450-02), NT3 (20 ng ml-1, PeproTech, 450-03), FGF4 (PeproTech, 100-31), FGF8 (PeproTech, 100-25), SAG (Millipore, 5666660), CHIR 099021 (Selleckchem, S1263), BMP4 (PeproTech, 120-05ET), BMP7 (PeproTech, 120-03P), LDN-193189 (S7507, Selleckchem), Activin A (50 ng/mL, PeproTech, 120-14P), SR11237 (100 nM, Tocris, 3411), dorsomorphin (DM, Sigma Aldrich P5499), SB (Tocris, 3748), Y-27643 (Selleckchem), L-ascorbic acid (FUJIFILM Wako Chemical Corporation, 344-44822), cAMP (Millipore Sigma, D0627).

value: hPS-derived medial pallium organoids

value: hMPO-CR

tag: differentiation age_(days)


title: human cerebellar organoids, cell line: 1208-2

description:
N5
10x 3' v3

source_name: hPS-derived cerebellar organoids

value: hPS-derived cerebellar organoids

value: hCbO


title: Eomes-ChIP-seq, miTSCs, biol rep 1

first: Abdenour

last: Soufi

address: 5 Little France Drive

institute: University of Edinburgh

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007279

value: Eomes (Abcam, ab23345)


title: Eomes-ChIP-seq, miTSCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-0072710


title: human medial pallium organoids, cell line: 2242-1

description:
N3
10x 3' v3


title: Gata3-ChIP-seq, miTSCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007278


title: human cerebellar organoids, cell line: KOLF

description:
N2
10x 3' v3

value: KOLF


title: GA-06-02407


title: IF-03-19418

value: Adrenal


title: Gata3-ChIP-seq, miTSCs, biol rep 1

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007277


title: human cerebellar organoids, cell line: 2242-1

description:
N1
10x 3' v3


title: Proximal, TCR

city: Philadelphia

first: Christoph

last: Ellebrecht

state: PA

address: 421 Curie Blvd, 1005 BRB

department: Dermatology

institute: University of Pennsylvania

description: HPG5bbz2-28-22filtered_feature_bc_matrix.h5

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation was performed with 10X genomics Cell Ranger v6.1.2
Assembly: human GENCODE v32/Ensembl 98 GRCh38 reference
Supplementary files format and content: H5
Library strategy: CITE-seq with TCR-seq

source_name: T cell

extract_protocol:
Proximal, distal, activated-undivided, and resting CARTs were isolated using fluorescence-activated cell sorting. 1.5x10^5 cells of each group were separately incubated in flow cytometry staining buffer (BioLegend) with a custom TotalSeq-C antibody cocktail in 100 ul for 30 minutes at 4C prior to washing three times. 10,000 live T cells from each LIPSTIC population were loaded onto NextGem K chips (10X Genomics) and processed in a 10X chromium device according to the manufacturer's recommendations.
Library preparation for gene expression, ADT, and TCR was performed using manufacturer's instructions using 10X 5' V2 protocol.

value: T cell


title: Input-ChIP-seq, miTSCs, biol rep 2

extract_protocol: ChIP-seq were carried out as described in Roberts, et al. Nat Cell Biol 23, 834–845 (2021). https://doi.org/10.1038/s41556-021-007276

value: Input DNA control


title: Proximal, ADT

library_source: other


title: GU-06-46615