title: PKR_RIPseq_auxin_plus_R2

data_processing:
For RIP-seq libraries, reads were first mapped to the hg38 build of mitochondrial and non-standard chromosomes using bowtie (-n2 -l 40 -X1000 -p 10 --best -3 1 --chunkmbs 1000) and only unaligned reads were processed further. Next, reads were aligned similarly to dm6 build of Drosophila genome to measure the spike return. The unaligned reads were then mapped to hg38 reference genome using STAR 2.7.3a with the following parameters to allow for multimapping of reads:  --runMode alignReads  --seedMultimapNmax 100000  --seedPerReadNmax 500  --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random  --outSAMattrIHstart 0  --alignWindowsPerReadNmax 50000  --alignTranscriptsPerReadNmax 50000  --alignTranscriptsPerWindowNmax 500  --seedPerWindowNmax 250  --seedNoneLociPerWindow 50  --outFilterMultimapNmax 1000  --winAnchorMultimapNmax 500
Assembly: hg38
Supplementary files format and content: bigWigs representing spike-normalized read coverage

extract_protocol:
For each RIP reaction, cells were trypsinized, counted and suspended in 1 ml of lysis buffer supplemented with protease, phosphatase and RNAse inhibitors (100 mM NaCl, 50 mM Tris-HCl, pH 7.5, 3 mM MgCl2, 0.5% IGEPAL CA-630) per 30 million cells (10 million cells each for J2-, PKR- and IgG-IP)
During the pre-clearing step, the lysate was treated additionally with TurboDNAse (Invitrogen/Thermo) and RNAse T1 (Thermo) to digest DNA and single stranded RNA respectively
The supernatant was collected using a magnetic rack and 7.5 µg of anti-dsRNA J2 antibody or 1.5 µg of anti-PKR antibody or 7.5 µg of anti-IgG (mouse) antibody was added to the supernatant, followed by incubation on rotating wheel for 2 hours at 4°C. Pre-blocked protein G dynabeads washed in lysis buffer were then added to each samples and allowed to be incubated at 4°C on a rotating wheel for 1 hour. This bead-antibody-lysate mix was then placed on magnet and washed 3X with the lysis buffer containing protease and RNAse inhibitors. After the last wash, beads were re-suspended in 1 ml Trizol buffer carrying 500,000 Drosophila S2 cells per ml for exogenous spike-in.
Since no RNA was detected in IgG samples, they were not processed further whereas the 75 ng of RNA per sample from J2 (N=3, +/- auxin, 4h) and PKR RIP (N=2, +/- auxin, 4h) was subjected to rRNA depletion using NEBNext rRNA depletion kit v2 (NEB). RNA was then cleaned using 2.2X Ampure bead purification to prevent loss of short RNA fragments. This was followed by 2.5 minutes of 98°C treatment for dissolving possible secondary structures. Next, cDNA library preparation was performed using NEBNext Ultra II Directional library kit (NEB). Final amplification of libraries was performed using 15 cycles based on qPCR-based amplification test performed for all libraries. Libraries were pooled in equimolar ratio and sequenced paired-end for 75 cycles on Nextseq550 using High-Output flow cell

value: Auxin, 500 µM, 4h

tag: rip antibody

value: IP with anti PKR antibody


title: RNAseq_4h_INTS1_AID_Auxin_Minus_R1

status: Public on Apr 16 2025

type: SRA

city: Boston

first: Apoorva

last: Baluapuri

state: MA

address: 45 Shattuck St.

department: Biological Chemistry and Molecular Pharmacology

country: USA

institute: Harvard Medical School

description:
Merged.DEseq.xlsx
RNAseq_4h_Minus_Auxin_F.bw
RNAseq_4h_Minus_Auxin_R.bw

library_source: transcriptomic

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 42 nt.
Samples were mapped to the Drosophila dm6 (spike) genome, and nonmapping reads subsequently mapped to hg38 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: hg38
Supplementary files format and content: Spreadsheets with normalized counts and associated analysis from DEseq2

molecule: total RNA

organism: Homo sapiens

source_name: embryonic kidney

growth_protocol: HEK293T cells were maintained in 5% FBS, 5% P/S DMEM

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse.
rRNA depleted RNA was used as input to the Illumina TruSeq stranded total RNA kit or NEB Next Ultra II Directional library prep kit using the manufacturer's protocol.
Stranded RNA-seq, dUTP

treatment_protocol: +/- Auxin (500 µM) 4h, 12h or untreated

tag: tissue

value: embryonic kidney

tag: cell line

tag: cell type

tag: genotype

value: homozygous miniAID

tag: treatment

value: 4h, Auxin_Minus


title: sample 243_genomic DNA from blood sample C1313

type: genomic

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Initial quality control was performed using GenomeStudio Methylation software. The raw intensity data files were imported into the R environment using the Bioconductor minfi package. Data satisfying detection P-values are 0.05 or more was regarded not applicable. Background correction with dye-bias normalization was performed using the normal-exponential out-of-band preprocessing method.
matrix processed value definition: Normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: blood sample of control patient

label_protocol: Standard Illumina Protocol

extract_protocol: The genomic DNA was extracted from all blood samples using a Maxwell® 16 Blood DNA Purification Kit (Promega, Madison, WI, USA).

tag: disease state

value: normal

tag: Sex

value: male

tag: age bracket

tag: blood sample id


title: sample 242_genomic DNA from blood sample C1305

value: female


title: PKR_RIPseq_auxin_plus_R1


title: PKR_RIPseq_auxin_minus_R2

value: Water, 4h


city: Shanghai

first: Heyu

last: Zhao

address: No.131 Dongan Road

country: China

institute: Fudan University

description:
Library name: sample23
20210415CZL-S60-3_BKDL210020494-1a-AK10029-N506

data_processing:
The transcriptomics data were processed by removing low-quality reads and calculating Q20, Q30, and GC content. Transcriptome data were aligned to the Mus musculus reference genome (GRCm38/mm10) using HISAT2.
Assembly: mm10
Supplementary files format and content: xlsx files

organism: Mus musculus

source_name: SNC Postnatal day 60_3

extract_protocol:
Cell samples for transcriptome sequencing were prepared according to the SMART-seq2 protocol. RNA integrity was assessed using the RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
The library was sequenced using an Illumina NovaSeq sequencer (Illumina, Inc., CA, USA), generating 150 bp paired end reads. A single sample generated raw data of approximately 6 GB. The RNA-seq samples were sent to Novogene Co., Ltd. (Beijing, China) for processing, library construction, and sequencing.

value: brain

value: dopaminergic neuron


title: sample 247_genomic DNA from blood sample C1366


description:
Library name: sample22
20210415CZL-S60-1_BKDL210020494-1a-AK13861-N506

source_name: SNC Postnatal day 60_1


title: PKR_RIPseq_auxin_minus_R1


title: sample 241_genomic DNA from blood sample C1294


title: sample 240_genomic DNA from blood sample C1293


description:
Library name: sample21
20210415CZL-N60-4_BKDL210020494-1a-AK22868-N506

source_name: NAC Postnatal day 60_4


title: J2_RIPseq_auxin_plus_R2

value: IP with anti J2 (dsRNA) antibody


title: J2_RIPseq_auxin_minus_R3


title: sample 239_genomic DNA from blood sample C1275


title: J2_RIPseq_auxin_minus_R1


description:
Library name: sample19
20210415CZL-N60-1_BKDL210020494-1a-AK14539-N506

source_name: NAC Postnatal day 60_1


title: PROseq_INTS1_auxin_plus_R3

description:
PROSeq_Auxin_Plus.binned.3pr_forward.spike_norm.bw
PROSeq_Auxin_Plus.binned.3pr_reverse.spike_norm.bw

data_processing:
FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the mm10 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl).
Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end position at single nucleotide resolution.
Data was normalized to spike-in reads and adjusted to account for variability in sequencing and spike batch.
Assembly: hg38
Supplementary files format and content: bigWigs representing spike-normalized read coverage

extract_protocol:
Cells were permeabilized as in Mimoso et al. 2024; run-ons were performed with biotinylated NTPs and then purified
Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.

treatment_protocol: +/- Auxin (500 µM) 4h, 10' 4sU label

tag: fraction

value: nascent RNA


title: J2_RIPseq_auxin_plus_R3


description:
Library name: sample20
20210415CZL-N60-3_BKDL210020494-1a-AK17668-N506

source_name: NAC Postnatal day 60_3


title: RNAseq_4h_INTS1_AID_Auxin_Minus_R2


title: J2_RIPseq_auxin_plus_R1


title: sample 237_genomic DNA from blood sample C1270


description:
Library name: sample18
20210224czl1-V30-3_BKDL210011248-1a-AK6759-N506

source_name: VTA Postnatal day 30_3


title: PROseq_INTS1_auxin_plus_R2


title: PROseq_INTS1_auxin_plus_R1


title: J2_RIPseq_auxin_minus_R2


title: sample 235_genomic DNA from blood sample C1262


description:
Library name: sample17
20210224czl1-V30-2_BKDL210011248-1a-AK13859-N506

source_name: VTA Postnatal day 30_2


title: PROseq_INTS1_auxin_minus_R3

description:
PROseq_Auxin_Minus.binned.3pr_forward.spike_norm.bw
PROseq_Auxin_Minus.binned.3pr_reverse.spike_norm.bw


title: TTseq_INTS8_auxin_plus_R2

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 42 nt.
Samples were mapped to the Drosophila dm6 (spike) genome, and nonmapping reads subsequently mapped to hg38 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: hg38
Supplementary files format and content: bigWigs representing DEseq-normalized read coverage

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded totl RNA kit using the manufacturer's protocol.
Stranded RNA-seq, dUTP

tag: labeling

value: 10 min 4sU label


title: TTseq_INTS8_auxin_plus_R3


title: sample 234_genomic DNA from blood sample C1260


description:
Library name: sample15
20210224czl1-S30-3_BKDL210011248-1a-AK14539-N506

source_name: SNC Postnatal day 30_3


title: PROseq_INTS1_auxin_minus_R2


title: PROseq_INTS1_auxin_minus_R1


title: sample 236_genomic DNA from blood sample C1268


title: sample 233_genomic DNA from blood sample C1259


title: sample 238_genomic DNA from blood sample C1274


title: TTseq_INTS8_auxin_plus_R1


description:
Library name: sample14
20210224czl1-S30-2_BKDL210011248-1a-AK5785-N506

source_name: SNC Postnatal day 30_2


title: TTseq_INTS8_auxin_minus_R2


description:
Library name: sample13
20210224czl1-S30-1_BKDL210011248-1a-AK9007-N506

source_name: SNC Postnatal day 30_1


title: sample 232_genomic DNA from blood sample C1251

source_name: blood sample of patient with major depressive disorder

value: major depressive disorder


title: TTseq_INTS8_auxin_minus_R1


title: TTseq_Parental_auxin_plus_R3

value: Parental


title: sample 231_genomic DNA from blood sample C1249


description:
Library name: sample12
20210224czl1-N30-3_BKDL210011248-1a-AK13858-N506

source_name: NAC Postnatal day 30_3


description:
Library name: sample11
20210224czl1-N30-2_BKDL210011248-1a-AK9824-N506

source_name: NAC Postnatal day 30_2


title: TTseq_Parental_auxin_plus_R1


title: TTseq_Parental_auxin_minus_R3


title: sample 230_genomic DNA from blood sample C1247


description:
Library name: sample10
20210224czl1-N30-1_BKDL210011248-1a-AK7343-N506

source_name: NAC Postnatal day 30_1


description:
Library name: sample16
20210224czl1-V30-1_BKDL210011248-1a-AK13860-N506

source_name: VTA Postnatal day 30_1


title: TTseq_Parental_auxin_minus_R2

source_name: embryonic kidney


title: sample 229_genomic DNA from blood sample C1241


title: TTseq_Parental_auxin_minus_R1


description:
Library name: sample9
20210408CZL1-V7-3_BKDL210018889-1a-AK6759-N503

source_name: VTA Postnatal day 7_3


title: TTseq_INTS1_auxin_plus_R2

description:
TTSeq_4h_Plus_Auxin_F.bw
TTSeq_4h_Plus_Auxin_R.bw


title: TTseq_INTS1_auxin_plus_R1


description:
Library name: sample8
20210408CZL1-V7-2_BKDL210018889-1a-AK13860-N503

source_name: VTA Postnatal day 7_2


title: TTseq_INTS1_auxin_minus_R3

description:
TTSeq_4h_Minus_Auxin_F.bw
TTSeq_4h_Minus_Auxin_R.bw


title: sample 227_genomic DNA from blood sample C1237


title: TTseq_INTS8_auxin_minus_R3


title: TTseq_INTS1_auxin_minus_R2


title: TTseq_INTS1_auxin_minus_R1


description:
Library name: sample7
20210408CZL1-V7-1_BKDL210018889-1a-AK13859-N503

source_name: VTA Postnatal day 7_1


description:
Library name: sample6
20210408CZL1-S7-3_BKDL210018889-1a-AK14539-N503

source_name: SNC Postnatal day 7_3


title: sample 225_genomic DNA from blood sample C1233

source_name: blood sample of control patient


title: patient-specific GABAergic neurons, AAV-sh1500, Repl1

city: Moscow

first: Evgenii

last: Lunev

address: Ulitsa Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology

data_processing:
TPM abundance estimates were generated with kallisto quant 0.44.0.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

source_name: iPSC-derived neurons

extract_protocol:
Total RNA was isolated using TRI Reagent (TR 118, Molecular Research Center, Cincinnati, OH) supplemented with BCP (B9673, Sigma-Adrich). Intact poly(A)+ RNA was extracted using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA)
Libraries were prepared using the Ultra II Directional RNA Library Prep Kit for Illumina and Unique Dual Index Primer Pairs (New England Biolabs)

value: iPSC-derived neurons


title: patient-specific GABAergic neurons, AAV-sh1500, Repl2


title: sample 224_genomic DNA from blood sample C1232


title: TTseq_Parental_auxin_plus_R2


description:
Library name: sample5
20210408CZL1-S7-2_BKDL210018889-1a-AK5785-N503

source_name: SNC Postnatal day 7_2


title: patient-specific GABAergic neurons, AAV-shSCR, Repl2

value: AAV-shSCR


title: patient-specific GABAergic neurons, AAV-shSCR, Repl1


title: patient-specific GABAergic neurons, AAV-shSCR, Repl3


title: sample 223_genomic DNA from blood sample C1231


title: patient-specific GABAergic neurons, AAV-GFP, Repl3

value: AAV-GFP


description:
Library name: sample4
20210408CZL1-S7-1_BKDL210018889-1a-AK9007-N503

source_name: SNC Postnatal day 7_1


description:
Library name: sample3
20210408CZL1-N7-3_BKDL210018889-1a-AK13858-N503

source_name: NAC Postnatal day 7_3


title: sample 222_genomic DNA from blood sample C1216


title: patient-specific GABAergic neurons, AAV-GFP, Repl2


title: TTseq_INTS1_auxin_plus_R3

value: embryonic kidney


title: patient-specific GABAergic neurons, AAV-GFP, Repl1


title: sample 228_genomic DNA from blood sample C1239


title: patient-specific GABAergic neurons, non-infected, Repl3

value: Control


title: sample 221_genomic DNA from blood sample C1205


description:
Library name: sample1
20210408CZL1-N7-1_BKDL210018889-1a-AK7343-N503

source_name: NAC Postnatal day 7_1


title: patient-specific GABAergic neurons, non-infected, Repl2


title: sample 226_genomic DNA from blood sample C1235


title: sample 220_genomic DNA from blood sample C1204


title: patient-specific GABAergic neurons, non-infected, Repl1


title: Neurons, Tbr1 dep, female, rep3

city: Philadelphia

first: Alekh

last: Paranjapye

state: Pennsylvania

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

description: Library name: shTbr1F3

data_processing:
Fastq files were aligned with STAR and assigned to genomic features using featureCounts.
Assembly: mm10
Supplementary files format and content: Aligned RNAseq read counts for all samples

source_name: wildtype e16.5 mouse embryos

growth_protocol: Cultured mouse neurons were grown using standard methods in neurobasal media supplemented with B27, GlutaMax, and Pen-strep on plates coated with poly-D-lysine.

extract_protocol:
Zymo Quick-RNA microprep
TruSeq Stranded mRNA

treatment_protocol: Neurons growth media was replaced with unsupplemented media and each triplicate of wells were infected with lentivirus containing shRNA against a specified target at doses independantly validated using RT-qPCR to deplete the target to ~50% levels. Virus containing media was removed and washed off on day in culture 6 and the neurons lysted at day in culture 10.

value: cultured neurons

value: WT

value: Tbr1 shRNA

value: Female


title: Neurons, Tbr1 dep, female, rep2

description: Library name: shTbr1F2


title: sample 219_genomic DNA from blood sample C1194

source_name: blood sample of patient with major depressive disorder

value: male


title: sample 218_genomic DNA from blood sample C1186

value: female


title: Neurons, Tbr1 dep, female, rep1

description: Library name: shTbr1F1


title: Neurons, Tbr1 dep, male, rep3

description: Library name: shTbr1M3

value: Male


title: IPTG.C1C2.Dex_rep2

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Center Dr

department: NCI

institute: NIH

description:
Library name: GH4790
GH4790

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NovaSeq output.
RNA-Seq reads were trimmed for adaptor sequence/low quality sequence using Cutadapt 1.18 with parameter options --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35
Trimmed sequence reads were mapped to mm10 genome using STAR 2.7.0f combined with the GENCODE (M21) annotation
Raw tag counts were obtained using featureCounts in subread 2.0.3 with parameter options:-s 2 -t exon -g gene_name --countReadPairs
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA were processed for extraction following the manufactor instruction (Nucleospin RNA extraction kit, Macherey-Nagel) and stored appropriately at -80°C.
Libraries were constructed according to the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: Mammary Adenocarcinoma Cells

value: IPTG inducible shNIPBL + NIPBL C1-C2 mutant

value: Dexametasone 100nM 2 hours


title: Neurons, Tbr1 dep, male, rep2

description: Library name: shTbr1M2


title: sample 217_genomic DNA from blood sample C1185

value: normal


title: Neurons, Setd5 dep, female, rep3

description: Library name: shSetd5F3

value: Setd5 shRNA


title: IPTG.C2.Dex_rep2

description:
Library name: GH4788
GH4788

value: IPTG inducible shNIPBL + NIPBL C2 mutant


title: IPTG.C1.Dex_rep2

description:
Library name: GH4787
GH4787

value: IPTG inducible shNIPBL + NIPBL C1 mutant


title: Neurons, Setd5 dep, female, rep2

description: Library name: shSetd5F2


title: Neurons, Setd5 dep, female, rep1

description: Library name: shSetd5F1


title: IPTG.EV.Dex_rep2

description:
Library name: GH4785
GH4785

value: IPTG inducible shNIPBL + EV


description:
Library name: sample2
20210408CZL1-N7-2_BKDL210018889-1a-AK9824-N503

source_name: NAC Postnatal day 7_2

value: brain

value: dopaminergic neuron


title: IPTG.WT.Dex_rep2

description:
Library name: GH4786
GH4786

value: IPTG inducible shNIPBL + NIPBL WT


title: Neurons, Setd5 dep, male, rep3

description: Library name: shSetd5M3

value: cultured neurons

value: WT


title: sample 216_genomic DNA from blood sample C1178

value: major depressive disorder


title: Neurons, Setd5 dep, male, rep2

description: Library name: shSetd5M2


title: sample 215_genomic DNA from blood sample C1170

value: male


title: Neurons, Med13l dep, female, rep3

description: Library name: shMed13lF3

value: Med13l shRNA

value: Female


title: noIPTG.EV.Dex_rep2

description:
Library name: GH4784
GH4784

value: Mammary Adenocarcinoma Cells


title: sample 214_genomic DNA from blood sample C1169

value: female


title: Neurons, Setd5 dep, male, rep1

description: Library name: shSetd5M1

value: Male


title: IPTG.C1C2.Dex_rep1

description:
Library name: GH4782
GH4782

value: IPTG inducible shNIPBL + NIPBL C1-C2 mutant

value: Dexametasone 100nM 2 hours


title: Neurons, Med13l dep, female, rep2

description: Library name: shMed13lF2


title: Neurons, Med13l dep, female, rep1

description: Library name: shMed13lF1


title: sample 213_genomic DNA from blood sample C1144

value: normal


title: IPTG.C2.Dex_rep1

description:
Library name: GH4780
GH4780

value: IPTG inducible shNIPBL + NIPBL C2 mutant


title: Neurons, Med13l dep, male, rep3

description: Library name: shMed13lM3


title: sample 212_genomic DNA from blood sample C1142


title: Neurons, Tbr1 dep, male, rep1

description: Library name: shTbr1M1

value: Tbr1 shRNA


title: Neurons, Med13l dep, male, rep1

description: Library name: shMed13lM1


title: Neurons, Mbd5 dep, female, rep2

description: Library name: shMbd5F2

value: Mbd5 shRNA


title: sample 211_genomic DNA from blood sample C1141


title: IPTG.WT.Dex_rep1

description:
Library name: GH4778
GH4778


title: IPTG.C1.Dex_rep1

description:
Library name: GH4779
GH4779

value: IPTG inducible shNIPBL + NIPBL C1 mutant


title: Neurons, Med13l dep, male, rep2

description: Library name: shMed13lM2


title: sample 210_genomic DNA from blood sample C1139


title: sample 209_genomic DNA from blood sample C1137


title: IPTG.EV.Dex_rep1

description:
Library name: GH4777
GH4777

value: IPTG inducible shNIPBL + EV


title: Neurons, Kmt2c dep, female, rep3

description: Library name: shKmt2cF3

value: cultured neurons

value: Kmt2c shRNA


title: noIPTG.EV.Dex_rep1

description:
Library name: GH4776
GH4776


title: Neurons, Mbd5 dep, male, rep2

description: Library name: shMbd5M2

value: WT


title: sample 208_genomic DNA from blood sample C1136

value: major depressive disorder

value: male


title: Neurons, Kmt2c dep, male, rep3

description: Library name: shKmt2cM3


title: sample 207_genomic DNA from blood sample C1133


title: Neurons, Kmt2c dep, female, rep1

description: Library name: shKmt2cF1

value: Female


title: Neurons, Kmt2c dep, female, rep2

description: Library name: shKmt2cF2


title: IPTG.C2.EtOH_rep2

description:
Library name: GH4701
GH4701

value: Mammary Adenocarcinoma Cells

value: Ethanol 2 hours


title: sample 206_genomic DNA from blood sample C1130


title: IPTG.C1C2.EtOH_rep2

description:
Library name: GH4703
GH4703


title: patient-specific GABAergic neurons, AAV-sh1500, Repl3

value: iPSC-derived neurons


title: Neurons, Kmt2c dep, male, rep1

description: Library name: shKmt2cM1

value: Male


title: Neurons, Kmt2c dep, male, rep2

description: Library name: shKmt2cM2


title: sample 205_genomic DNA from blood sample C1124

value: female


title: IPTG.C1.EtOH_rep2

description:
Library name: GH4700
GH4700


title: Neurons, Kdm6b dep, female, rep3

description: Library name: shKdm6bF3

value: Kdm6b shRNA


title: Neurons, Mbd5 dep, female, rep3

description: Library name: shMbd5F3


title: Neurons, Mbd5 dep, female, rep1

description: Library name: shMbd5F1


title: Neurons, Mbd5 dep, male, rep3

description: Library name: shMbd5M3


title: sample 204_genomic DNA from blood sample C1123

value: normal


title: Neurons, Kdm6b dep, female, rep2

description: Library name: shKdm6bF2


title: IPTG.WT.EtOH_rep2

description:
Library name: GH4699
GH4699

value: IPTG inducible shNIPBL + NIPBL WT


title: Neurons, Mbd5 dep, male, rep1

description: Library name: shMbd5M1

value: Mbd5 shRNA


title: sample 203_genomic DNA from blood sample C1110


title: Neurons, Kdm6b dep, female, rep1

description: Library name: shKdm6bF1


title: Neurons, Kdm6b dep, male, rep3

description: Library name: shKdm6bM3


title: Neurons, Kdm6b dep, male, rep2

description: Library name: shKdm6bM2


title: noIPTG.EV.EtOH_rep2

description:
Library name: GH4697
GH4697


title: Neurons, Dnmt3a dep, female, rep3

description: Library name: shDnmt3aF3

value: Dnmt3a shRNA


title: Neurons, Kdm6b dep, male, rep1

description: Library name: shKdm6bM1


title: sample 201_genomic DNA from blood sample C1098


title: IPTG.C1C2.EtOH_rep1

description:
Library name: GH4695
GH4695

value: IPTG inducible shNIPBL + NIPBL C1-C2 mutant


title: IPTG.C2.EtOH_rep1

description:
Library name: GH4693
GH4693

value: IPTG inducible shNIPBL + NIPBL C2 mutant


title: Neurons, Dnmt3a dep, female, rep1

description: Library name: shDnmt3aF1

value: cultured neurons


title: sample 202_genomic DNA from blood sample C1109


title: Neurons, Dnmt3a dep, male, rep3

description: Library name: shDnmt3aM3

value: WT


title: Neurons, Dnmt3a dep, male, rep2

description: Library name: shDnmt3aM2


title: sample 200_genomic DNA from blood sample C1097


title: Neurons, Dnmt3a dep, male, rep1

description: Library name: shDnmt3aM1


title: sample 199_genomic DNA from blood sample C1096


title: Neurons, Chd8 dep, female, rep3

description: Library name: shChd8F3

value: Chd8 shRNA


title: Neurons, Chd8 dep, female, rep2

description: Library name: shChd8F2


title: IPTG.C1.EtOH_rep1

description:
Library name: GH4692
GH4692

value: IPTG inducible shNIPBL + NIPBL C1 mutant


title: sample 198_genomic DNA from blood sample C1095


title: IPTG.EV.EtOH_rep2

description:
Library name: GH4698
GH4698

value: IPTG inducible shNIPBL + EV


title: IPTG.WT.EtOH_rep1

description:
Library name: GH4691
GH4691

value: Mammary Adenocarcinoma Cells


title: IPTG.EV.EtOH_rep1

description:
Library name: GH4690
GH4690

value: Ethanol 2 hours


title: sample 197_genomic DNA from blood sample C1094

value: major depressive disorder


title: Neurons, Chd8 dep, male, rep3

description: Library name: shChd8M3

value: Male


title: Neurons, Ash1l dep, female, rep3

description: Library name: shAsh1lF3

value: Ash1l shRNA

value: Female


title: Neurons, Chd8 dep, female, rep1

description: Library name: shChd8F1


title: sample 196_genomic DNA from blood sample C1093

value: normal

value: male


title: Neurons, Chd8 dep, male, rep2

description: Library name: shChd8M2


title: noIPTG.EV.EtOH_rep1

description:
Library name: GH4689
GH4689


title: Neurons, Dnmt3a dep, female, rep2

description: Library name: shDnmt3aF2


title: vehicle tumor 3

city: ann arbor

first: gary

last: luker

state: MI

address: 109 zina pitcher place

department: radiology

institute: university of michigan

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt

source_name: breast tumor

growth_protocol: E0771 mouse breast cancer cells grown as orthotopic tumor implants in female syngeneic C57BL/6J mice

extract_protocol:
Tumors removed from mice; digested with collagenase/DNAse I in Miltenyi OctoDissociator; following lysis of red blood cells, isolation of CD45+ cells with immunomagnetic beads; recovered cells used at a ratio of 3:2 CD45+ to CD45- cells for DropSeq single cell RNA sequencing
bar coded single cells with polyA enrichment for RNA for sequencing

treatment_protocol: Mice treated with combination balixafortide/anti-PD-1 antibody; balixafortide only; anti-PD-1 antibody only; or matched vehicles

value: breast tumor

value: female

value: vehicle


title: sample 195_genomic DNA from blood sample C1079


title: Neurons, Ash1l dep, female, rep1

description: Library name: shAsh1lF1


title: vehicle tumor 2


title: Neurons, Ash1l dep, male, rep3

description: Library name: shAsh1lM3


title: sample 194_genomic DNA from blood sample C1075


title: Neurons, Ash1l dep, male, rep1

description: Library name: shAsh1lM1


title: vehicle tumor 1


title: Neurons, Ash1l dep, male, rep2

description: Library name: shAsh1lM2


title: Neurons, Nontargetting Control, female, rep2

description: Library name: NTF2

value: Nontargetting control shRNA


title: anti-PD-1 tumor 3


title: sample 192_genomic DNA from blood sample C1072


title: anti-PD-1 tumor 2


title: Neurons, Nontargetting Control, female, rep1

description: Library name: NTF1

value: cultured neurons


title: sample 191_genomic DNA from blood sample C1064


title: Neurons, Chd8 dep, male, rep1

description: Library name: shChd8M1

value: WT


title: anti-PD-1 tumor 1


title: Neurons, Nontargetting Control, male, rep2

description: Library name: NTM2


title: sample 190_genomic DNA from blood sample C1063


title: Neurons, Ash1l dep, female, rep2

description: Library name: shAsh1lF2


title: Neurons, No virus, female, rep2

description: Library name: NVF2

value: No virus


title: sample 189_genomic DNA from blood sample C1059


title: Neurons, No virus, female, rep1

description: Library name: NVF1


title: Neurons, No virus, male, rep3

description: Library name: NVM3


title: balixafortide tumor 2

value: balixafortide


title: sample 193_genomic DNA from blood sample C1074


title: sample 188_genomic DNA from blood sample C1052


title: Neurons, Nontargetting Control, female, rep3

description: Library name: NTF3


title: sample 187_genomic DNA from blood sample C1048


title: Neurons, No virus, male, rep1

description: Library name: NVM1


title: balixafortide/anti-PD-1 tumor 3


title: TKO_None_None_r2

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

description: Library name: XZVJ31

library_source: genomic

data_processing:
Fasta sequence files were analysed for quality using FastQC v0.11.9. Remaining adaptor sequences and low-quality sequence fragments were removed using fastp v0.20.1 with the parameters –length_required 25, –cut_tail, –cut_tail_window_size 4, –cut_tail_mean_quality 20, –disable_quality_filtering. Filtered reads were aligned to the human hg38 genome using STAR v2.7.5a without gene annotation GTF file, with the parameters –alignIntronMax 1, –alignEndsType Extend5pOfReads12 –alignMatesGapMax 2000, –outFilterMatchNminOverLread 0.50, –outFilterScoreMinOverLread 0.50, and filtering for properly paired mates with a mapq score of 40 or above and duplicates were marked using Picard.
deepTools AlignmentSieve with parameter –ATACshift was used to adjust sequencing pairs by +5 and −4 base pairs to account for the 9 bp shift introduced at Tn5 insert sites. Genome-wide sequencing coverage was calculated using deepTools v3.5.0 bamCoverage function and then converted to bigWig tracks that were normalized by counts per million (CPM) in each sample
Assembly: hg38
Supplementary files format and content: bigWig format for read density, normalized by counts per million

growth_protocol: K-562 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, penicillin and streptomycin

extract_protocol:
ATAC-seq procedure was performed using the Active Motif kit (catalog # 53150) and manufacturer recommendations were followed. 50,000 cells were used per sample.
The Active Motif kit used generates sequencing-ready libraries

treatment_protocol: Cells were treated with BRM014 at 10 micromolar for 6 hours or left untreated

tag: biological replicate

tag: genetic modification

value: TKO


title: TKO_None_BRM014_r2

description: Library name: XZVJ32


title: sample 185_genomic DNA from blood sample C1040


title: balixafortide tumor 3


title: balixafortide/anti-PD-1 tumor 2


title: balixafortide/anti-PD-1 tumor 1


title: WT_None_None_r2

description: Library name: XZVJ27

value: Parental


title: Neurons, No virus, female, rep3

description: Library name: NVF3


title: TKO_None_BRM014_r1

description: Library name: XZVJ24


title: TKO_None_None_r1

description: Library name: XZVJ23


title: Neurons, Nontargetting Control, male, rep1

description: Library name: NTM1


title: sample 183_genomic DNA from blood sample C1019


title: Col8a2Q455K/Q455K/Tcf4+/- mice, Tcf4 knockout, rep3

city: Kyotanabe

first: Taisuke

last: Numao

state: Kyoto

department: Department of Biomedical Engineering, Faculty of Life and Medical Sciences

institute: Doshisha University

data_processing:
Sequencing data quality was assessed using FastQC (version 0.12.1) to evaluate read quality, GC content, and sequence duplication levels
Low-quality reads and adapter sequences were removed using fastp (version 0.23.2)
Filtered reads were mapped to the mouse reference genome (GRCm39) using Spliced Transcripts Alignment to a Reference (STAR) software (version 2.7.10a)
Gene expression was quantified using RNA-Seq by Expectation-Maximization (RSEM) program (version 1.3.3)
Differential gene expression analysis was performed using DESeq2 (Bioconductor version 3.19)
Assembly: GRCm39
Supplementary files format and content: Gene quantification data output from RSEM analysis with normalized expression values

source_name: cornea

extract_protocol:
Total RNA was extracted from corneal endothelial cells using RNAlater and the RNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. RNA quantity and quality were assessed using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit.
RNA sequencing libraries were prepared using the SMART-Seq HT Kit (Takara Bio Inc.) following the manufacturer's protocol. After full-length cDNA synthesis, Illumina libraries were prepared using NexteraXT (Illumina Inc.).

value: cornea

value: primary

value: corneal endothelial cells

value: Tcf4 heterozygous knockout


title: WT_None_BRM014_r1

description: Library name: XZVJ20


title: Col8a2Q455K/Q455K/Tcf4+/- mice, Tcf4 knockout, rep2


title: balixafortide tumor 1


title: sample 182_genomic DNA from blood sample C1005

value: major depressive disorder


title: KK22-H-225

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

description: 10x Genomics

data_processing:
Demultiplexing and preprocessing of the spatial transcriptomics data was conducted with SpaceRanger v1.3.0.
After converting the raw 10X data to fastq format with SpaceRanger's mkfastq, the data was aligned against the human reference transcriptome GRCh38 2020-A with the SpaceRanger count function using default values.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files (features and barcode data), matrix files (expression data), PNG image data of the tissue per sample, tissue positions and scalefactor file (json format) from SpaceRanger pipeline
Library strategy: Visium FFPE spatial transcriptomics

source_name: Human ETMR tumor

extract_protocol:
FFPE tissue blocks of ETMR tumors from distinct patients were submitted to neuropathology review and analyzed for RNA quality. Three tissue sections of distinct tumors with up to 6.5 x 6.5 mm2 were selected for placement on the mRNA capture areas of a Visium Gene Expression slide for FFPE (2000233, 10x Genomics), fixed in methanol and H&E stained according to the Visium Gene expression for FFPE user guide (CG000409 Rev A, 10x Genomics). Brightfield histology images were taken using a 4x objective on a Nikon Eclipse Ni (5254 x 5396 pixels). Raw images were stitched together using NIS-Elements (Nikon) and exported as .tiff files with high-resolution settings.
Libraries were prepared following the Visium Spatial Gene expression for FFPE user guide (G000407 Rev A, 10x Genomics) and library size and concentration were measured using a Tapestation 2000 (Agilent Technologies, Inc). The library was sequenced with a sequencing depth of approximately 25,000 pair-reads per spot in the following read protocol: read 1: 28 cycles; i7 index read: 10 cycles; i5 index read: 10 cycles; and read 2: 50 cycles

value: brain tumor

tag: molecular information

tag: age


title: sample 181_genomic DNA from blood sample C1002

value: male


title: Col8a2Q455K/Q455K/Tcf4+/- mice, Tcf4 knockout, rep1


title: Neurons, No virus, male, rep2

description: Library name: NVM2

value: Male


title: FB-Organoid D48 hETMR (BT-183) Carbo 10µM

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v6.0.2.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the human reference transcriptome GRCh38 with the CellRanger count function using default values. Additionally, samples KK22-H-243, KK22-H-266 and KK22-H-267 were also aligned against the combined human+murine reference GRCh38-and-mm10-2020-A.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoid

extract_protocol:
Cell dissociation using papain/DNAse solution, with incubation for 60min for organoids. Cell dissociation of 2D culture using Accutase and Trypsin EDTA for all conditions. Organoid samples had consistently > 90% vitality in manual counting, so they were not submitted to FACS sorting.
Approximately 10,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced separately by the NextSeq2000 sequencing platform.
scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: organoid

value: hiPSCs + BT-183

value: Carboplatin 10µM

tag: treatment time


title: WT_None_BRM014_r2

description: Library name: XZVJ28


title: sample 186_genomic DNA from blood sample C1044

value: normal

value: female


title: KK22-H-224

description: 10x Genomics


title: KK22-H-226

description: 10x Genomics


title: Col8a2Q455K/Q455K mice, control, rep3


title: FB-Organoid D48 hETMR (BT-183) DMSO

description: 10x Genomics

value: DMSO


title: FB-Organoid D48 no tumor DMSO

description: 10x Genomics

value: hiPSCs


title: Col8a2Q455K/Q455K mice, control, rep2


title: FB-Organoid D30 ETMR BT-183 CP-673451

description: 10x Genomics


title: FB-Organoid D30 ETMR BT-183 DMSO

description: 10x Genomics


title: FB-Organoid D30 hETMR (BT-183) Etoposide 1µM

description: 10x Genomics

value: Etoposide 1µM


title: sample 180_genomic DNA from blood sample C1001


title: WT_None_None_r1

description: Library name: XZVJ19

value: Parental


title: FB-Organoid D30 hETMR (BT-183) Carbo 10µM

description: 10x Genomics


title: Col8a2Q455K/Q455K mice, control, rep1

value: cornea


title: sample 179_genomic DNA from blood sample C1000


title: PBS1, PCV2d-infected, scRNA seq

city: xianyang

first: chen

middle: yun

last: long

state: shaanxi

address: yangling

institute: Northwest A & F University

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope  (https://github.com/singleron-RD/CeleScope)  pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS.
scRNA-seq libraries were constructed according to Singleron GEXSCOPE protocol by GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies)

value: Lung

tag: infection


title: sample 184_genomic DNA from blood sample C1034


title: FB-Organoid D48 hETMR (BT-183) Etoposide 1µM

description: 10x Genomics

tag: tissue


title: sample 178_genomic DNA from blood sample C0998


title: Neurons, Nontargetting Control, male, rep3

description: Library name: NTM3

value: cultured neurons

value: WT

value: Nontargetting control shRNA


title: sample 177_genomic DNA from blood sample C0997


title: FB-Organoid D30 hETMR (BT-183) DMSO

description: 10x Genomics

tag: cell line


title: sample 176_genomic DNA from blood sample C0996


title: Combo-5P, mRNA-derived cDNA

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description: 10x Genomics

data_processing:
Gene expressing reads were aligned to the mm10 genome (mouse) using the 10x Genomics Cell Ranger, with the pipeline cellranger count or multi.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Disscociated tumor cells were loaded into a Chromium Controller (10x Genomics).
10x Chromium Next GEM Single Cell 5' Reagent Kits V2

value: Combo


title: sample 173_genomic DNA from blood sample C0989

value: male


title: sample 175_genomic DNA from blood sample C0994

value: major depressive disorder


title: FB-Organoid D30 no tumor DMSO

description: 10x Genomics

value: organoid


title: Control-5P, mRNA-derived cDNA

description: 10x Genomics

value: Control


title: FB-Organoid D30 Control GFP+ iPSCs

description: 10x Genomics

value: GFP+-hiPSCs + BT-183


title: PBS0, control, scRNA seq

value: control


title: FB-Organoid D30 BT-183 GFP+ iPSCs

description: 10x Genomics

value: GFP+-hiPSCs


title: Type 2 nueroblast-derived neurons and glia 17

city: Eugene

first: Chris

last: Doe

state: Oregon

address: 1585 E 13th Ave

institute: University of Oregon

description: Library name: Sample 17

data_processing:
Our bioinformatic analysis was performed using pipeline from Fluent BioSciences, Parse Bioscience, and the Seurat R package (Hao et al., 2024; Satija et al., 2015). Briefly, pipelines from Fluent BioSciences and Parse Biosciences were used to perform demultiplexing, alignment, filtering, counting of barcodes and UMIs with an output being a cell-by-genes matrix of counts. We aligned our sequences to a custom reference genome by adding flpD5 (RRID:Addgene_32132), redstinger (RRID:Addgene_46165), and unc84sfGFP (RRID:Addgene_46023) (+SV40 tail) sequences and annotations to the Drosophila genome release BDGP6.32.109.
Assembly: Drosophila genome release BDGP6.32.109
Supplementary files format and content: T2.atlas.rds Atlas of neurons and glia derived from Type 2 neuroblasts
Supplementary files format and content: T2.atlas.glia.rds Atlas of glia derived from Type 2 neuroblasts
Supplementary files format and content: T2.atlas.neurons.rds Atlas of neurons derived from Type 2 neuroblasts

organism: Drosophila melanogaster

source_name: central brain

extract_protocol:
The samples were flash-frozen in liquid nitrogen and stored separately at -80°C. Nuclei dissociated from the frozen, dissected brains was performed according to published protocols (McLaughlin et al., 2022).
We first used the split-pool method (Parse Bioscience, Seattle, WA, USA) to barcode RNAs from whole brain to generate a library which includes both T1 and T2 progeny. This library, T1+T2, was used for analysis in Figure 1 and 5. To increase the number of T2 nuclei for snRNAseq, we labeled T2 nuclei by crossing 20xUAS-FLPG5.PEST;worniu-gal4,asense-gal80; Act5c(FRT.CD2)gal4  to UAS-RedStinger (RFP) or UAS-unc84-2xGFP (GFP) flies. The adult flies were aged for 1 week at 25 ˚C before dissection. Equal amounts of male and female central brains (excluding optic lobes) were dissected at room temperature within 1 hour. The samples were flash-frozen in liquid nitrogen and stored separately at -80°C. Nuclei dissociated from the frozen, dissected brains was performed according to published protocols (McLaughlin et al., 2022). RFP+ or GFP+ nuclei were collected by sorting dissociated nuclei with SONY-SH800 with 100 μm chip. We performed three rounds of sorting and snRNAseq. In the first round, we pooled male and female brains together to select GFP+ nuclei and used particle-templated instant partitions to capture single nuclei to generate cDNA library (Fluent BioSciences, Waterton, MA). In the second round, RFP+ nuclei from male and female were pooled together. In the third round, RFP+ nuclei from male and female brains were collected separately. The split-pool method was then used to generate barcoded cDNA libraries from each individual nucleus from the second and third rounds. All libraries were sequenced with pair-ends reads 150bp on Illumina Novaseq 6000 (University of Oregon's Genomics and Cell Characterization Core Facility).

value: central brain

tag: cell type

value: total RNA

value: paired-end


title: Type 2 nueroblast-derived neurons and glia 15

description: Library name: Sample 15

tag: genotype


title: Type 2 nueroblast-derived neurons and glia 18

description: Library name: Sample 18

tag: treatment


title: Type 2 nueroblast-derived neurons and glia 16

description: Library name: Sample 16


title: Type 2 nueroblast-derived neurons and glia 19

description: Library name: Sample 19


title: KRASi-5P, mRNA-derived cDNA

description: 10x Genomics

value: KRASi


title: E7R54_O304LL

city: Umeå

first: Emanuel

last: Holm

address: Johan Bures Väg 12

department: MTB

country: Sweden

institute: Umeå University

data_processing:
FastQC for quality control
Mapping to mouse genome (mm10, UCSC) using STAR
Assembly: Mm10 from UCSC
Supplementary files format and content: tab-delimited text file counts for each Sample

source_name: Liver

extract_protocol:
RNeasy Plus Universal minikit (Qiagen, #73404)
NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770)

value: Liver

tag: strain


title: Hi-C_contact heatmap_Yeast nuclei_SynAZFa_10 kb resolation

city: Tianjin

first: Yue

last: Liu

address: 92 Weijin Road, Nankai District

institute: Tianjin University

description: Hi-C: The normalized contact heatmap of Yeast nuclei_SynAZFa, by chromosomes, with 11-kb resolution.

data_processing:
Assembly: S288C with SynAZFa
Supplementary files format and content: text file
*data processing step

organism: Saccharomyces cerevisiae

extract_protocol: Yeast nuclei were fixed with 1% formaldehyde for 10 min at room temperature, and the crosslinking reaction was quenched with 0.2 M glycine for 5 min.


title: sample 172_genomic DNA from blood sample C0985

data_processing:
Initial quality control was performed using GenomeStudio Methylation software. The raw intensity data files were imported into the R environment using the Bioconductor minfi package. Data satisfying detection P-values are 0.05 or more was regarded not applicable. Background correction with dye-bias normalization was performed using the normal-exponential out-of-band preprocessing method.
matrix processed value definition: Normalized Average Beta

extract_protocol: The genomic DNA was extracted from all blood samples using a Maxwell® 16 Blood DNA Purification Kit (Promega, Madison, WI, USA).

tag: disease state

tag: Sex

value: female


title: Type 2 nueroblast-derived neurons and glia 13

description: Library name: Sample 13


title: Type 2 nueroblast-derived neurons and glia 14

description: Library name: Sample 14


title: NSD2i-5P, mRNA-derived cDNA

description: 10x Genomics

value: Lung


title: Hi-C_contact heatmap_Yeast_SynAZFa_10 kb resolation

description: Hi-C: The normalized contact heatmap of Yeast_SynAZFa, by chromosomes, with 10-kb resolution.

extract_protocol:
Yeast were fixed with 3% formaldehyde for 20 min at room temperature, and the crosslinking reaction was quenched with 0.375 M glycine for 15 min. The crosslinked cells were incubated with lysozyme at 37°C for 10min to lyse the cells.
A Hi-C library was prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.


title: sample 170_genomic DNA from blood sample C0977

value: normal

tag: age bracket

tag: blood sample id


title: sample 171_genomic DNA from blood sample C0984


title: Hi-C_contact heatmap_Yeast_Control_10 kb resolation

description: Hi-C: The normalized contact heatmap of Yeast_Control, by chromosomes, with 11-kb resolution.

data_processing:
The Hi-C data regarding Yeast_SynAZFa and isolated nuclei were mapped iteratively to a combination of the S288C genome and SynAZFa sequence using the ICE software package (version 1f8815d0 cc9e). After filtering out dangling ends and other unusable data, the valid pairs were binned into 10-kb nonoverlapping genomic intervals to generate contact maps. The contact maps were normalized using an iterative method to eliminate systematic biases.
Assembly: S288C with SynAZFa
Supplementary files format and content: text file
*data processing step


title: E7R53_O304RML

value: WT


title: Type 2 nueroblast-derived neurons and glia 12

description: Library name: Sample 12


title: sample 174_genomic DNA from blood sample C0991


title: E7R52_CDHFD

value: CDHFD


title: H3K4me3 ChIP_Yeast nuclei_SynAZFa_rep2

description:
H3K4me3 ChIP-seq of SynAZFa in isolated yeast.
test.fa

library_source: other

data_processing:
Assembly: S288C with SynAZFa
Supplementary files format and content: tdf file
*data processing step

molecule: other

extract_protocol:
Samples were cross-linked with 1% formaldehyde for 10 minutes at room temperature and the crosslinking reaction was then quenched by the addition of glycine.
A standard ChIP-seq protocol (Kim and Dekker, 2018) was carried out using an H3K4me3 antibody (9751S, Cell Signaling Technology)。


title: Type 2 nueroblast-derived neurons and glia 20

description: Library name: Sample 20


title: E7R51_RD

value: RD


title: H3K4me3 ChIP_Yeast nuclei_SynAZFa_rep1


title: sample 169_genomic DNA from blood sample C0972

value: male


title: Type 2 nueroblast-derived neurons and glia 10

description: Library name: Sample 10


title: E7R50_O304LL


title: E7R49_O304RML


title: sample 166_genomic DNA from blood sample C0962

value: major depressive disorder


title: Type 2 nueroblast-derived neurons and glia 9

description: Library name: Sample 9


title: sample 168_genomic DNA from blood sample C0967


title: H3K4me3 ChIP_Yeast_SynAZFa_rep2

description:
H3K4me3 ChIP-seq of SynAZFa in yeast.
test.fa


title: E7R48_CDHFD


title: sample 167_genomic DNA from blood sample C0963


title: H3K4me3 ChIP_Yeast_Control_rep2

description:
H3K4me3 ChIP-seq of yeast harboring PRS416 plasmid as control.
test.fa


title: sample 165_genomic DNA from blood sample C0960


title: E7R47_RD


title: sample 164_genomic DNA from blood sample C0955


title: H3K4me3 ChIP_Yeast_Control_rep1

data_processing:
Trimmomatic (version 0.36) was used to filter out low-quality reads. Clean reads were mapped to the reference genome by Bwa (version 0.7.15). Samtools (version 1.3.1) was used to remove potential PCR duplicates. MACS2 software (version 2.1.1.20160309) was used to call peaks. The mapped bam files were finally converted to Bigwig format via bamCoverage using RPKM normalization for visualization.
Assembly: S288C with SynAZFa
Supplementary files format and content: tdf file
*data processing step


title: Type 2 nueroblast-derived neurons and glia 7

description: Library name: Sample 7


title: Type 2 nueroblast-derived neurons and glia 6

description: Library name: Sample 6


title: E7R46_O304RML


title: ATACseq_Yeast nuclei_SynAZFa_rep2

description:
ATAC-seq of SynAZFa in isolated yeast nuclei.
test.fa

extract_protocol:
Samples were lysed in prechilled lysis buffer (15 mM Tris-HCl pH 7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 5 mM 2-ME and 0.2% Triton X-100) for 10 min at 4°C.
Cell pellets were lysed via incubation for 10 min at 4°C on the rotation mixer. DNA ragmentation by Tn5 was carried out according to standard protocols (Corces et al., 2017).


title: Type 2 nueroblast-derived neurons and glia 11

description: Library name: Sample 11


title: Type 2 nueroblast-derived neurons and glia 5

description: Library name: Sample 5


title: E7R45_O304LL


title: Type 2 nueroblast-derived neurons and glia 4

description: Library name: Sample 4


title: sample 162_genomic DNA from blood sample C0952


title: H3K4me3 ChIP_Yeast_SynAZFa_rep1


title: E7R44_CDHFD


title: sample 160_genomic DNA from blood sample C0947


title: Type 2 nueroblast-derived neurons and glia 3

description: Library name: Sample 3


title: ATACseq_Yeast_SynAZFa_rep2

description:
ATAC-seq of SynAZFa in yeast.
test.fa


title: E7R42_O304RML


title: sample 161_genomic DNA from blood sample C0950


title: ATACseq_Yeast_SynAZFa_rep1

description:
ATAC-seq of SynAZFa in yeast.
test.fa


title: E7R43_RD


title: E7R41_O304LL


title: Type 2 nueroblast-derived neurons and glia 2

description: Library name: Sample 2


title: E7R40_CDHFD


title: timepoint_4, multiseq

city: San Francisco

first: Sara

last: Sunshine

address: 1700 4th Street

institute: University of California, San Francisco

description: 10x Genomics

data_processing:
GEX FASTQ files were pre-processed using 10X Genomics CellRanger v3.1
MULTI-seq FASTQ files were processed using the deMULTIplex R package (McGinnis et al. 2019)
Assembly: custom: hg38 and mm10 reference genome concatenated with the Respiratory Syncytial Virus genome (GenBank: M74568.1)
Supplementary files format and content: cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gx
Supplementary files format and content: cellbarcode_multiseq_ID_match.tsv.gz containing cell barcode IDs matched to multiseq IDs;  multiseq_sampleid_key_barcodes.csv.gz containing MULTI-seq barcodes matched to sample IDs

organism:
Homo sapiens
Mus musculus

extract_protocol:
Treated cells were washed with 1X PBS and dissocated with trpysin. Spike-in murine 3T3 cells were added to dissociated samples. Single-cell suspensions were washed and subsequently labelled with MULTI-seq lipid-modified barcodes (as described in McGinnis et al. 2019).
We performed library prep folling manufactuerer's protocols (10X Genomics). Modifications to protocol were made for MULTI-seq library preparation as described in McGinnis et al. 2019.

treatment_protocol: A549 cells were infected with Respiratory Syncytial Virus (RSV). Controls cells were treated with heat-inactivated RSV or vehicle control.

value: RSV

tag: time

value: 12 hpi

tag: spike-in

value: murine 3T3 cells


title: sample 159_genomic DNA from blood sample C0946


title: ATACseq_Yeast_Control_rep2

description:
ATAC-seq of yeast harboring PRS416 plasmid as control.
test.fa


title: RNA-seq_Yeast_SynAZFa_rep3

description:
RNA-seq of SynAZFa in yeast.
Saccharomyces_R64_plasmid.fa

extract_protocol:
Total RNA from yeast was purified according to the instructions for the Qiagen RNeasy Mini Kit (QIAGEN, Germany).
Reverse transcription was performed using the First Strand cDNA Synthesis Kit (GeneCopoeia, USA).


title: Type 2 nueroblast-derived neurons and glia 1

description: Library name: Sample 1


title: timepoint_3, multiseq

description: 10x Genomics

value: 8 hpi


title: ATACseq_Yeast_Control_rep1


title: sample 157_genomic DNA from blood sample C0937


title: ATACseq_Yeast nuclei_SynAZFa_rep1


title: E7R39_RD


title: sample 163_genomic DNA from blood sample C0954


title: sample 156_genomic DNA from blood sample C0932


title: RNA-seq_Yeast_SynAZFa_rep2


title: timepoint_2, multiseq

description: 10x Genomics

value: 4 hpi


title: E3R38_O304


title: sample 155_genomic DNA from blood sample C0928


title: RNA-seq_Yeast_SynAZFa_rep1


title: timepoint_1, multiseq

description: 10x Genomics

value: 0 hpi


title: RNA-seq_Yeast_Control_rep3

description:
RNA-seq of yeast harboring PRS416 plasmid as control.
Saccharomyces_R64_plasmid.fa


title: sample 154_genomic DNA from blood sample C0922


title: sample 158_genomic DNA from blood sample C0938


title: E3R37_O304


title: E3R36_O304


title: RNA-seq_Yeast_Control_rep2


title: sample 153_genomic DNA from blood sample C0911


title: sample 152_genomic DNA from blood sample C0909


title: sample 151_genomic DNA from blood sample C0904


title: E3R35_O304


title: DNA-seq of SynAZFa in yeast

description:
Deep sequencing of SynAZFa in yeast with average depth is 400 x.
AZFa3-1.sort.fa

data_processing:
Clean reads were mapped to the reference genome by Bwa (version 0.7.10) and the SNP and InDel were deteced by GATK (v3.4.0).
Assembly: S288C with SynAZFa
Supplementary files format and content: tdf file
*data processing step
Library strategy: WGS

extract_protocol: Yeast genome DNA preparation for genome sequencing was described as Narayana Annaluru et al. Science344,55-58(2014).


title: RNA-seq_Yeast_Control_rep1

data_processing:
The reference genome was indexed for mapping using hisat2 (version 2.0.5), after which Stringtie (version 2.0) was used to quantify the gene expression levels. The mapped bam files were converted to the Bigwig format using bamCoverage from Deeptools (version 3.3.1). Afterward, the Bam files were visualized in the IGV. The differentially expressed genes were called using DESeq2 (R package, version 1.26.0) in R (version 3.6.0).
Assembly: S288C with SynAZFa
Supplementary files format and content: tdf file
*data processing step


title: timepoint_2, gex

description: 10x Genomics


title: E3R34_O304


title: E3R33_CDHFD


title: sample 150_genomic DNA from blood sample C0902


title: WT_2years_3

city: Madiosn

first: Romeo

middle: S

last: Blanc

state: WI

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

department: CRB

institute: University of Wisconsin-Madison

description: WT 20mo post tmx

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 subread-2.0.1, featurecounts, -s 0 -t exon -g gene_name
Read Quantification3 salmon-1.5.2, --seqBias --gcBias --posBias
Assembly: mg39 + Gencode-M27 Annotation
Supplementary files format and content: gene counts

source_name: Skeletal muscle

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols.

value: Skeletal muscle

value: Muscle stem cell

value: Kmt5afl/fl ; Pax7+/+

value: 5 x Tmx (IP) as control

value: 2 years


title: E3R32_CDHFD

value: Liver


title: Type 2 nueroblast-derived neurons and glia 8

description: Library name: Sample 8

value: central brain

value: total RNA

value: paired-end


title: timepoint_3, gex

description: 10x Genomics


title: WT_2years_1_WT_2years_2

description: WT 20mo post tmx


title: sample 149_genomic DNA from blood sample C0892

source_name: blood sample of control patient

value: normal

value: female


title: B73xW22_DS_R3

city: Duesseldorf

first: Thomas

last: Hartwig

address: University Street 1

institute: Heinrich-Heine University

description: Library name: 150

data_processing:
library strategy: MNase-defined cistrome-Occupancy Analysis (MOA-seq)
Reads were filtered using SeqPurge (v2022-07-15) with parameters “-min_len 20 -qcut 0” (Sturm et al. 2016).
Due to the short fragment length in MOA, read pairs almost completely overlapped. MOA-seq paired-end reads were merged into single-end reads, including base quality score correction, using NGmerge (v0.3) (Gaspar 2018) with parameters “-p 0.2 -m 15 -d -e 30 -z -v”.
Reads were mapped to the diploid genome (or the separate genomes for inbred data) using STAR (v2.7.7a). As STAR was originally designed to map RNA, we set the flag --alignIntronMax 1 for DNA (no introns allowed) as well as parameters “--outSAMmultNmax 2, --winAnchorMultimapNmax 100, and -outBAMsortingBinsN 5 (Dobin et al. 2013).
Bam files were converted to bed format using bamToBed (Quinlan and Hall 2010).
Format conversion and the calculation of the average mapped fragment length (AMFL) was done using SAMtools (v1.9) (Li et al. 2009).
The effective genome size was calculated using unique-kmers.py (https://github.com/dib-lab/khmer/) with AFML and respective genome fasta as inputs.
The function genomeCoverageBed of Bedtools (v2.29.0) was then used to convert the bed files to bedgraph, scaled by the quotient of the effective genome size and the number of uniquely mapped reads (reads per genome coverage, RPGC).
BigWig files for visualization were generated using bedGraphToBigWig (Kent et al. 2010).
During this study the maize inbred A619 had no reference assembly. Of the inbred maize lines with high quality assemblies, A619 is most closely related to Oh43 (Flint‐Garcia et al.2005). We downloaded approximately 30x coverage of A619 WGS data from NCBI SRA (SRR8997919, SRR10127976, SRR8907067, SRR5725670, SRR5663982, and SRR5663981) and then mapped it to the Oh43 genome using bwa-mem2 (v2.2.1) (Li and Durbin 2009). Only uniquely mapping reads (q30) were retained. The GATK4 pipeline in combination with the “best practices workflow” (https://gatk.broadinstitute.org/hc/en-us/sections/360007226651) was used to identify initial A619/Oh43 SNPs and INDELs with the hard filtering settings: “QD < 2.0”, "QUAL < 100.0", "SOR > 3.0", "FS > 60.0", and "MQ < 40.0". We used these initial variants for base- and variant-recalibration, followed by two additional rounds of training based on convolutional neural networks (CNN) to optimize filtration settings (training input setting: “prior=15.0" and “tranche=99”) and, ultimately selected a refined set of biallelic, homozygous A619/Oh43 SNPs and INDELs. G2Gtools (v. 0.2.7, https://churchill-lab.github.io/g2gtools/) was employed to integrate SNPs and INDELs into the Oh43 genome and generate a A619 pseudo-reference fasta and gff3 file. The average SNP mismatch rate of respective MOA reads from the F1 to the B73xA619 genome was 0.1%, only twice that of the average high-quality B73xNAM genomes (0.04-0.05%), and substantially lower than mapping to either B73 or the A619 psuedo-reference alone (~0.54%).
Assembly: Diploid genomes were created by concatenating the B73 V5 genome with the respective paternal genome (NAM v1 / 2 genomes (Hufford et al. 2021), Mo17 CAU v1, W22 v2 (Springer et al. 2018), A188 v1 (Lin et al. 2021), and A619 see separate entry).
Supplementary files format and content: Bed files containing significantly enriched sites on both parental genomes
Supplementary files format and content: BigWig files containing MOA-seq files on both parental genomes

organism: Zea mays

source_name: leaf blade

growth_protocol: Plants were grown at 28C until the V4 stage, which is when treatment began

extract_protocol:
Nuclei extraction and DNase treatment for MOA-seq was performed as decribed in Savadel et al. 2021
Libraries were constructed as decribed in Savadel et al. 2021

treatment_protocol: Plants were subjected to drought treatment or well-watered treatment for 86h

value: leaf blade

value: DS


title: B73xW22_DS_R2

description: Library name: 149


title: timepoint_1, gex

description: 10x Genomics

value: RSV

value: murine 3T3 cells


title: E3R30_CDHFD

value: WT

value: CDHFD


title: WT_2wks_3

description: WT 2wks post tmx

value: Skeletal muscle


title: timepoint_4, gex

description: 10x Genomics

value: 12 hpi


title: B73xW22_DS_R1

description: Library name: 148


title: sample 147_genomic DNA from blood sample C0883

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai


title: E3R29_CDHFD


title: E3R28_RD

value: RD


title: WT_2wks_2

description: WT 2wks post tmx

value: Muscle stem cell

value: Kmt5afl/fl ; Pax7+/+

value: 5 x Tmx (IP) as control


title: WT_2wks_1

description: WT 2wks post tmx


title: sample 146_genomic DNA from blood sample C0882

value: male


title: KO_6wks_3

description: KO 6wks post tmx

value: Kmt5afl/fl ; Pax7CreERT2/+

value: 5 x Tmx (IP) to induce KO


title: sample 145_genomic DNA from blood sample C0878

value: normal


title: sample 144_genomic DNA from blood sample C0875


title: KO_6wks_2

description: KO 6wks post tmx


title: E3R26_RD

value: Liver


title: sample 143_genomic DNA from blood sample C0874

value: female


title: B73xTx303_DS_R3

description: Library name: 144

value: leaf blade

value: DS


title: KO_6wks_1

description: KO 6wks post tmx


title: B73xW22_WW_R2

description: Library name: 146

value: WW


title: sample 142_genomic DNA from blood sample C0873


title: sample 148_genomic DNA from blood sample C0887


title: E3R25_RD

value: WT


title: B73xTx303_DS_R1

description: Library name: 142


title: B73xW22_WW_R1

description: Library name: 145


title: B73xW22_WW_R3

description: Library name: 147


title: sample 141_genomic DNA from blood sample C0872

value: major depressive disorder


title: TLS, 120h, batch 2

city: Dresden

first: Ryan

middle: George

last: Savill

address: Pfotenhauer Strasse 108

institute: Max Planck Institute for Molecular Cell Biology and Genetics

data_processing:
Cell Ranger pipeline version 3 (10x Genomics) was used to de-multiplex the raw base call files, generate fastq files, map to the mouse reference genome mm10, filter the alignment and count barcodes and unique molecular identifiers. To de-multiplex samples within our single MULTI-Seq scRNA-seq dataset, we used the deMULTIplex R package (version 1.0.2). In short, sample IDs were assigned to cells. Cells with no associated sample barcode (unassigned (unable to provide a sample identity using the deMULTIplex algorithm) and negative (cells without barcode), as well as cells with more than one barcode (doublets) were removed for downstream analysis. After preprocessing, the two scRNA-seq runs for time-point 120h were merged into one single object. Initial QC was performed with Seurat (version 4.3.0). Single-cell data generated were loaded with a minimum requirement of 3 cells and 200 features (default parameters). Subsequently, cells with unique feature counts < 2,000 & > 80,000 (48h and 120h); < 500 & > 80,000 (72h and 96h) and a mitochondrial fraction above 5% were discarded from the analysis. The Seurat objects after QC were then used for cluster determination. This procedure was performed individually per each time-point. Subsequently, the expression data were independently normalized, and variable features within the three datasets were detected, log-normalized and scaled to 10,000 (default settings). A list of cell cycle markers was used to score for cell cycle stage and to subsequently scale the data with regression out (var.to.regress) of S and G2M phase-related genes. For downstream analysis and visualization of the datasets, a PCA followed by a UMAP (dims=1:30, n.neighbors=10) were run, and clusters were identified using the Louvain algorithm. Next, we manually inspected the distribution of UMI counts, total RNA counts, mitochondrial and ribosomal fraction for each cluster at individual time-points. Based on this additional QC step we removed spurious clusters. Specifically, for 48h, two clusters (one with low n cells (<10) & one with low mitochondrial fraction) were removed, followed by reclustering; for 96h a small cluster was removed with a low mitochondrial and high ribosomal fraction, followed by reclustering; for 120h, a putative doublet cluster (shown by almost double amount of total RNAs counts and UMIs) was removed. The remaining clusters were then further annotated using a combination of classifiers and manual curation to ensure most accurate and reliable annotation of cell states. While for 48h, 96h and 120h the clusters identified by the Louvain algorithm were readily interpretable in terms of marker genes, this proved more challenging for the 72h samples. We therefore first used a publicly available mouse reference atlases (E6.5 to E8.5) to predict the in vivo cell ID using scmap. In short, a table of the top variable features across the reference dataset was obtained, and relevant markers were chosen with a criterion of passing the threshold of log fold change of 0.5, and a p-value of 1e-5. Following the curation of the relevant marker table, the top 200 markers were chosen in each reference cluster to train a classifier. The query dataset was then converted to an sce (SingleCellExperiment) object, and the classifier was applied to the query atlas – after filtering to include only the relevant stages (E6.5 and E7.5). Finally, the 72h object was re-clustered using a list of the top 20 marker genes (obtained using the FindAllMarkers function in Seurat with default settings, except for pseudocount.use=0.1) for all in vivo cell types identified by the classifier (FindNeighbors, dims=1:10 and FindClusters, resolution=0.4). To subcluster the 120h cluster with a pluripotency signature, the cluster was subsetted and re-clustered (FindNeighbors, dims=1:10 and FindClusters, resolution=0.05).
Assembly: mm10
Supplementary files format and content: The CellRanger output files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary files format and content: df48_final.rds is a processed Seurat file of the 48h cells that passed QC, with metadata, raw counts, normalised counts, PCA and UMAP dimensionality reductions, neighbourhood graphs, clusterings and phenotypic features.
Supplementary files format and content: df72_final.rds is a processed Seurat file of the 72h cells that passed QC, with metadata, raw counts, normalised counts, PCA and UMAP dimensionality reductions, neighbourhood graphs, clusterings and phenotypic features.
Supplementary files format and content: df96_final.rds is a processed Seurat file of the 96h cells that passed QC, with metadata, raw counts, normalised counts, PCA and UMAP dimensionality reductions, neighbourhood graphs, clusterings and phenotypic features.
Supplementary files format and content: df120_final.rds is a processed Seurat file of the 120h cells that passed QC, with metadata, raw counts, normalised counts, PCA and UMAP dimensionality reductions, neighbourhood graphs, clusterings and phenotypic features.

source_name: 120h TLS

growth_protocol: Mouse Embryonic Stem Cells (mESCs) carrying a T::H2B-mCherry and Sox2::H2B-Venus reporter (Veenvliet et al., Science 2020) were cultured under standard Serum+LIF+feeder conditions (400 mL Knockout Dulbecco’s Modified Eagle’s Medium (DMEM) (4500 mg/ml glucose, w/o sodium pyruvate) (Gibco) supplemented with  75 mL ES cell tested FCS, 5 ml 100x L-glutamine (200 nM) (Lonza #BE17-605E), 5 mL 100x penicillin (5000 U/ml)/ streptomycin (5000 μg/ml), 5 ml 100x non-essential amino acids (Gibco #11140-35),  1 mL 500x β-mercaptoethanol (5mM, 1000x Invitrogen),  5 mL 100x nucleosides (Chemicon) and 5µl 10000x of Murine Leukemia Inhibitory Factor (LIF) (Sigma-Aldrich, #ESG1107) on 6cm plates (Sarstedt, # 83.3901.300) coated with 0.1% gelatin and a layer of mitotically inactive fibroblasts. Culture medium was refreshed every 24h and mESCs were split using Trypin-EDTA (Thermofisher, #ESG1107) in a dilution of 1:10 every 48h. The cells were passaged twice before proceeding to TLS formation. Gastruloids and TLSs for were generated following the previously published protocol (Veenvliet et al., Science 2020; Bolondi et al., Bio Prot 2021). In short, mESCs were feeder-freed by sequential plating of the cells on 0.1% gelatin-coated 6-well plates and incubating the cells at 37ºC for 25’, 20’ and 15’ respectively. Cells were then washed with 5mL pre-warmed PBS supplemented with MgCl2 + NaCl (PBS+/+) (Sigma, #D8662-500mL), spun down for 5’ at 300g, followed by a second wash with 5mL of pre-warmed NDiff227 medium (Takara). After pelleting (5’, 300g) and gentle trituration in 500µl NDiff227, cells were counted using an automatic cell counter (Invitrogen™ Countess™ 3 FL Automated Cell Counter) and diluted in NDiff227 to a final concentration 10 cells/µl. 30µl of the cell suspension (~300 cells) were then plated into individual wells of a ultra-low attachment U-bottom 96 well plate (Costar, #7007) using a multichannel pipette, and placed in an incubator (37ºC, 5% CO2). After 48h, the aggregates were pulsed with 3μM CHIR99021 (CHIR) (Tocris, #4423) diluted in 150µl NDiff227 per sample. At 72h, 150µl medium was refreshed with new pre-incubated NDiff227. Between 92h-96h (96h for all samples used for integrated molecular-phenotypic profiling), TLS formation was initiated by supplementing the gastruloids with 5% (final v/v) Growth-factor-Reduced Matrigel (Corning #356231) diluted in NDiff227 medium.

extract_protocol:
Gastruloids and trunk-like-structures were generated as described in Veenvliet et al., Science 2020. Following wide-field imaging, 72 structures at 48h, 48 at 72h, 24 at 96h and 24 at 120h were picked with a p200 cut tip and transferred in a new well of a 96-well plate. Next, structures were washed twice with ice cold PBS and trypsinized in 20µl TrypLE Express (Gibco) for 25 minutes in the incubator at 37°C, pipetting every 5 minutes to help dissociation. Multi-seq labeling was then performed as previously described (McGinnis et al., Nature Methods 2019; Lopéz-Anguita et al., Development 2022). Briefly, single-cell suspensions of each sample were incubated with a unique BC-Lipid modified oligonucleotide “anchor” mix (200nM each final) 5 minutes on ice. Next, a 200nM “co-anchor” mix was added to each sample and cells were incubated for an additional 5 minutes on ice. The reaction was then quenched by addition of 200µl 1xPBS/1%BSA, and cell suspensions were then washed twice with 1xPBS/1%BSA in the plate. Next, all samples for each day were pooled in a 1.5 ml DNA lowBind tube in 1xPBS/1%BSA, and cells pelleted by centrifugation. The recovered cells were resuspended in 1xPBS/0.4%BSA, counted and then subjected to 10x single-cell RNA-seq using the 10x Genomics Chromium™ Single Cell 3’ v3.1 (one reaction for gastruloid pool at 48, 72, and 96h; two reactions for TLS pool at 120h).
Following MULTI-seq barcode labeling, single-cell RNA-seq (scRNA-seq) experiments were performed as previously described (McGinnis et al., Nature Methods 2019; Lopéz-Anguita et al., Development 2022).  Briefly, single-cell suspensions were subjected to GEMs encapsulation and libraries generated according to the manual to recover the cDNA fraction. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were sequenced with a minimum of 400 million paired end fragments according to parameters described in the manual. To recover the Multi-seq barcodes, two modifications were introduced in the standard workflow: (i) during the cDNA amplification step 1µl of an oligonucleotide to enrich for the MULTI-seq BCs was added to the reaction and (ii) after cDNA amplification and incubation with SPRIselect beads, the Multi-seq BCs containing supernatant was collected and subjected to further SPRIselect beads incubation in order to recover the Multi-seq BCs as previously described (McGinnis et al., Nature Methods 2019). Multi-seq BCs recovery and integrity were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. The obtained material was then used as input for Multi-seq BCs library preparation (performed as described in Lopéz-Anguita et al., Development 2022). Briefly, 10ng input material obtained from the 10x cDNA purification (see section above) was used to perform library PCR using KAPA HiFi HotStart ReadyMix (Roche, KK2601) in 50µl reaction with the following steps: 95ºC 5 minutes/ 98ºC 15sec – 60ºC 30sec – 72ºC 30sec (13 cycles)/ 72ºC 1 minutes/ 4ºC hold. Next, AMPure XP beads (Beckman, A63881) cleanup (1.6X) was performed to purify the Multi-seq BC libraries. Quality and concentration of the obtained libraries were measured using Agilent High Sensitivity D5000 ScreenTape on an Agilent 4150 TapeStation. Libraries were then sequenced using asymmetric end sequencing (150 cycles kit; 28/91 FC-410-1002) on a Novaseq platform at a minimum of 50 million fragments per sample.

value: 120h TLS

value: F1G4  mESCs

value: differentiated mESCs


title: KO_2years_3

description: KO 20mo post tmx

value: Skeletal muscle

value: Muscle stem cell

value: 2 years


title: B73xTx303_DS_R2

description: Library name: 143


title: B73xTx303_WW_R3

description: Library name: 141


title: sample 140_genomic DNA from blood sample C0869

address: 35, Shinano-machi

institute: Keio University School of Medicine


title: TLS, 120h, batch 1


title: KO_2years_1

description: KO 20mo post tmx


title: B73xTx303_WW_R2

description: Library name: 140


title: E3R27_RD

value: RD


title: KO_2wks_3

description: KO 2wks post Tmx

value: Kmt5afl/fl ; Pax7CreERT2/+


title: gastruloids, 96h

source_name: 96h gastruloid

value: 96h gastruloid


title: sample 139_genomic DNA from blood sample C0863


title: E3R24_RD


title: B73xTx303_WW_R1

description: Library name: 139


title: sample 138_genomic DNA from blood sample C0847

value: normal


title: KO_2wks_2

description: KO 2wks post Tmx

value: 5 x Tmx (IP) to induce KO


title: gastruloids, 48h

source_name: 48h gastruloid

value: 48h gastruloid


title: B73xP39_DS_R3

description: Library name: 138

value: leaf blade


title: gastruloids, 72h

source_name: 72h gastruloid

value: 72h gastruloid


title: KO_2wks_1

description: KO 2wks post Tmx


title: sample 136_genomic DNA from blood sample C0835

value: male


title: sample 137_genomic DNA from blood sample C0837


title: B73xP39_DS_R2

description: Library name: 137

value: DS


title: KO_2years_2

description: KO 20mo post tmx


title: B73xP39_DS_R1

description: Library name: 136


title: WGBS_Mouse_1cell_SynAZFa_rep2

description:
WGBS of SynAZFa in mouse 1cell embryos.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf

data_processing:
Assembly: mm9 (without chrY)+S288C+hg18 chrY:12,952,206-14,101,944
Supplementary files format and content: BigWig
*data processing step

extract_protocol:
Twenty embryos were collected for each sample and lysed by incubation at 37°C for 1 h.
Bisulfite conversion was performed on cell lysates using an EZ DNA Methylation-Gold Kit. (Zymo).


title: S. aureus, ATCC 25923, Treatment_2, Day 1

city: Singapore

first: Guobin

last: Qi

address: 5A Engineering Drive 1

country: Singapore

institute: NUS，Chemical & Biomolecular Engineering

description: Library name: TPA2PyBu-2

data_processing:
Illumina NovaSeq 6000 was used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. RPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: ASM1342v1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: Matrix table with RPKM values for every gene and every sample.

organism: Staphylococcus aureus

source_name: S. aureus, ATCC 25923

extract_protocol:
Total RNA was extracted using the mirVana™ miRNA Isolation Kit (Ambion-1561) following the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, NR604-02) following the manufacturer's protocols.

value: S. aureus, ATCC 25923


title: WGBS_Mouse_1cell_SynAZFa_rep3


title: S. aureus, ATCC 25923, Treatment_3, Day 1

description: Library name: TPA2PyBu-3


title: B73xP39_WW_R3

description: Library name: 135

value: WW


title: sample 134_genomic DNA from blood sample C0831

source_name: blood sample of patient with major depressive disorder

value: major depressive disorder


title: sample 135_genomic DNA from blood sample C0832

value: female


title: WGBS_Mouse_1cell_SynAZFa_rep1

data_processing:
All bisulfite sequencing reads were first trimmed to remove adaptors and low-quality bases using Trimmomatic (version 0.3.6). All the reads that passed quality control were mapped to the reference genome using Bismark (version 0.16.3). Only reads with a unique mapping location in the genome were retained for further analysis. The DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated), which was produced by the Bismark toolkit  of bismark_methylation_extractor.
Assembly: mm9 (without chrY)+S288C+hg18 chrY:12,952,206-14,101,944
Supplementary files format and content: BigWig
*data processing step


title: B73xP39_WW_R2

description: Library name: 134


title: S. aureus, ATCC 25923，Control_3, Day 1

description: Library name: Con-3

value: control


title: RNA-seq_Mouse_Morula_SynAZFa_rep2

description:
RNA-seq of SynAZFa in mouse Morula parthenogenetic embryos.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf

data_processing:
Assembly: mm9 (without chrY)+S288C+hg18 chrY:12,952,206-14,101,944
Supplementary files format and content: tdf file
*data processing step

extract_protocol:
The zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1788). Embryos were washed in M2 medium and then lysed in 2 μL of lysis buffer containing RNase inhibitor.
All RNA-seq libraries were generated following the Smart-seq2 protocol.


title: sample 133_genomic DNA from blood sample C0830


title: B73xP39_WW_R1

description: Library name: 133


title: RNA-seq_Mouse_Morula_SynAZFa_rep1


title: sample 132_genomic DNA from blood sample C0785


title: sample 131_genomic DNA from blood sample C0773


title: S. aureus, ATCC 25923，Control_2, Day 1

description: Library name: Con-2


title: S. aureus, ATCC 25923，Control_1, Day 1

description: Library name: Con-1


title: RNA-seq_Mouse_Morula_Control_rep2

description:
RNA-seq of Control (non-injected) in mouse Morula parthenogenetic embryos.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf


title: B73xOh43_DS_R3

description: Library name: 132


title: sample 130_genomic DNA from blood sample C0770


title: RNA-seq_Mouse_Morula_Control_rep1


title: B73xOh43_DS_R2

description: Library name: 131


title: RNA-seq_Mouse_4cell_SynAZFa_rep2

description:
RNA-seq of SynAZFa in mouse 4-cell parthenogenetic embryos.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf


title: S. aureus, ATCC 25923, Treatment_1, Day 1

description: Library name: TPA2PyBu-1


title: sample 129_genomic DNA from blood sample C0760


title: B73xOh43_DS_R1

description: Library name: 130


title: B73xOh43_WW_R3

description: Library name: 129


title: sample 128_genomic DNA from blood sample C0757


title: sample 127_genomic DNA from blood sample C0746


title: B73xOh43_WW_R2

description: Library name: 128


title: B73xOh43_WW_R1

description: Library name: 127


title: RNA-seq_Mouse_4cell_Control_rep2

description:
RNA-seq of Control (non-injected) in mouse 4-cell parthenogenetic embryos.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf


title: RNA-seq_Mouse_4cell_Control_rep1


title: Melanocytes (HEM-ad), UVA-irradiated, 8-oxoG_CD-seq

city: Grand Rapids

first: Gerd

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE., 5352W/Phase2

department: Center for Epigenetics

institute: Van Andel Research Institute

description: Library name: 5_HEM-ad_UVA_8oxoG

data_processing:
Fastq files containing sequencing reads were trimmed from the 3’ end to 2x80 nucleotide length using Trim_Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned to the hg19 reference genome using BWA-MEM with default parameters.
Duplicate alignments were marked and removed with the ‘removeDups’ SAMBLASTER option.
Only divergently aligned pairs of reads with a single nucleotide gap between reads were selected by selecting SAM records with TLEN of 3 and saved as bam files for downstream analyses. TLEN=3 represents divergently aligned reads with 1 nucleotide between mates.
To visualize the reads, bam files were visualized using the Integrative Genomics Viewer version 2.8.9. The tracks were displayed with a ‘view as pairs’ option to show pairs together with a line joining the ends.
Assembly: hg19
Supplementary files format and content: Chromosome name, position of damaged base, and trinucleotide sequences (5'-N-damaaged base-N) were written to a tab-delimited text file.

source_name: foreskin

growth_protocol: Human primary melanocytes were grown on collagen-coated plates (1.67 μg/ml gelatin) using the MGM-4 melanocyte growth medium Bullet Kit (Lonza, Cat. CC-3249) and incubated in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Genomic DNAs were isolated using Quick-DNA Miniprep Plus Kit (Zymo Research; Irvine, CA) according to the manufacturer’s instruction manual.
Genomic DNAs were framgmeted to an averge length of 300 bp and circuliarized with T4 DNA ligase at 16°C overnight. Non-circularized linear DNAs were removed with Plasmid-Safe ATP-Dependent DNAse treatment. To generate DNA double-strand breaks at CPD or 8-oxoG lesions, the circularized DNAs were treated with T4-PDG or Fpg and APE1 followed by S1 nuclease to create double-strand breaks with ligatable ends. A-tailed with Klenow fragment exo- (NEB) and then adaptors were ligated with NEBNext Ultra II Ligation Master Mix and followed by incubation with USER enzyme (NEB). The purified DNA libraries were amplified by PCR with NEBNext Ultra II Q5 Master mix and NEBNext i5 and i7 primers and used for DNA sequencing.

treatment_protocol: To induce DNA damage, human primary melanocyte cells were irradiated with several dose of UVA or UVB.

value: foreskin

value: Primary melanocytes (HEM-ad)

value: Primary human epidermal melanocyte (adult)

value: Wild type

value: UVA (72 J/cm2)

tag: batch


title: Melanocytes (Hermes-4a), UVA-irradiated, 8-oxoG_CD-seq

description: Library name: 5_Hermes-4a_UVA_8oxoG

value: human melanocytes, telomerase immortalized


title: Melanocytes (HEM-neo), UVA-irradiated, 8-oxoG_CD-seq

description: Library name: 5_HEM-neo_UVA_8oxoG

value: Primary melanocytes (HEM-neo)

value: Primary human epidermal melanocyte (neonatal)


title: Melanocytes (HEM-neo), no UV-irradiated control, 8-oxoG_CD-seq

description: Library name: 5_HEM-neo_NT_8oxoG


title: RNA-seq_Mouse_2cell_SynAZFa_rep2

description:
RNA-seq of SynAZFa in mouse 2-cell parthenogenetic embryo.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf


title: sample 125_genomic DNA from blood sample C0720


title: sample 126_genomic DNA from blood sample C0734


title: B73xOh7B_DS_R2

description: Library name: 125

value: leaf blade


title: Melanocytes (HEM-neo), UVA-irradiated, CPD_CD-seq, 5 hours incubated

description: Library name: 4_HEM-neo_UVA_5h_CPD

value: UVA (72 J/cm2), 5 hours incubation


title: sample 124_genomic DNA from blood sample C0704

value: normal


title: RNA-seq_Mouse_2cell_SynAZFa_rep1


title: B73xOh7B_DS_R1

description: Library name: 124

value: DS


title: RNA-seq_Mouse_1cell_SynAZFa_rep2

description:
RNA-seq of SynAZFa in mouse 1-cell parthenogenetic embryo.
Mus_musculus_mix_v4_noYM_chr.fa, Mus_musculus_mix_v4_noYM.gtf


title: Melanocytes (Hermes-3a), UVA-irradiated, 8-oxoG_CD-seq

description: Library name: 5_Hermes-3a_UVA_8oxoG


title: RNA-seq_Mouse_4cell_SynAZFa_rep1


title: sample 123_genomic DNA from blood sample C0700

value: male


title: B73xOh7B_WW_R3

description: Library name: 123

value: WW


title: sample 122_genomic DNA from blood sample C0689

value: major depressive disorder


title: RNA-seq_Mouse_1cell_SynAZFa_rep1

data_processing:
Paired-end RNA-seq reads were trimmed and then mapped to the reference genome by TopHat v2.0.12. HTSeq v.0.6.0 was used to calculate the counts of each gene, and  RPKM was used to assess the expression level. IGV was used to view the mapping results.
Assembly: mm9 (without chrY)+S288C+hg18 chrY:12,952,206-14,101,944
Supplementary files format and content: tdf file
*data processing step


title: B73xOh7B_WW_R2

description: Library name: 122


title: WT_2years_10X

description: WT 20mo post tmx

data_processing:
demultiplexing: cellranger 7.0.1 mkfastq ran using default parameters
cell and gene counting: cellranger 7.0.1count ran using default parameters
Assembly: 10X provided mm10-2020-A reference
Supplementary files format and content: compressed folders containing barcode, feature, and matrix files for each sample. Generated as part of the outputs via cellranger count

extract_protocol:
Extraction is included within the 10X genomics scRNA protocol
Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR.

value: Skeletal muscle

value: Muscle stem cell

value: Kmt5afl/fl ; Pax7+/+

value: 5 x Tmx (IP) as control


title: Melanocytes (HEM-neo), UVA-irradiated, CPD_CD-seq, 3 hours incubated

description: Library name: 4_HEM-neo_UVA_3h_CPD

value: foreskin

value: UVA (72 J/cm2), 3 hours incubation


title: B73xOh7B_WW_R1

description: Library name: 121


title: sample 121_genomic DNA from blood sample C0687

data_processing:
Initial quality control was performed using GenomeStudio Methylation software. The raw intensity data files were imported into the R environment using the Bioconductor minfi package. Data satisfying detection P-values are 0.05 or more was regarded not applicable. Background correction with dye-bias normalization was performed using the normal-exponential out-of-band preprocessing method.
matrix processed value definition: Normalized Average Beta

value: female


title: Melanocytes (HEM-neo), UVA-irradiated, CPD_CD-seq, 0 hour incubated

description: Library name: 4_HEM-neo_UVA_0h_CPD

value: Wild type

value: UVA (72 J/cm2), 0 hour incubation


title: B73xOh7B_DS_R3

description: Library name: 126


title: sample 120_genomic DNA from blood sample C0679


title: Melanocytes (Hermes-3a), UVA-irradiated, CPD_CD-seq, 0 hour incubated

description: Library name: 4_Hermes-3a_UVA_0h_CPD

value: human melanocytes, telomerase immortalized


title: sample 119_genomic DNA from blood sample C0676


title: WT_2wks_10X

description: WT 2wks post tmx


title: Melanocytes (Hermes-3a), UVA-irradiated, CPD_CD-seq, 5 hours incubated

description: Library name: 4_Hermes-3a_UVA_5h_CPD


title: Melanocytes (HEMn-LP, light-pigmented), UVB-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 3_HEMn-LP_UVB_CPD

value: Primary melanocytes (HEMn-LP)

value: primary human melanocyte (neonatal, light-pigmented)


title: B73xNC358_DS_R2

description: Library name: 119

value: leaf blade


title: B73xNC358_DS_R3

description: Library name: 120

value: DS


title: KMT5aKO_2years_10X

description: KO 20mo post tmx

value: Kmt5afl/fl ; Pax7CreERT2/+

value: 5 x Tmx (IP) to induce KO


title: KMT5aKO_6wks_10X

description: KO 6wks post tmx


title: Melanocytes (HEMn-LP, light-pigmented), UVA-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 3_HEMn-LP_UVA_CPD

value: UVA (72 J/cm2)


title: KMT5aKO_2wks_10X

description: KO 2wks post Tmx

value: Skeletal muscle


title: B73xNC358_DS_R1

description: Library name: 118


title: Melanocytes (HEMn-LP, light-pigmented), no UV-irradiated control, CPD_CD-seq (UVA vs. UVB)

description: Library name: 3_HEMn-LP_NT_CPD


title: sample 117_genomic DNA from blood sample C0645

value: major depressive disorder

value: male


title: Melanocytes (Hermes-3a), UVA-irradiated, CPD_CD-seq, 3 hours incubated

description: Library name: 4_Hermes-3a_UVA_3h_CPD


title: B73xNC358_WW_R3

description: Library name: 117

value: WW


title: siRNA GSK3A+GSK3B -GM-MØ - Donor C

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads.Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each sample

source_name: Monocyte-derived GM-CSF macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10e6 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 5 days with 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-MØ). Cells were then transfected with siRNA control (siCNT), siRNA for GSK3A (siGSK3A), siRNA for GSK3B (siGSK3B) or both (siGSK3A and siGSK3B) and analyzed 72 hours later.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 5 days in RPMI 10% FBS containing GM-CSF. Fully-differentiated macrophages were transfected (HiPerFect, QIAgen) with a human GSK3A-specific siRNA (siGSK3A, Dharmacon), GSK3B-specific siRNA (siGSK3B, Dharmacon) or both (siGSK3A and siGSK3B). Silencer Select Negative Control No. 2 siRNA (siCNT) (Dharmacon) was used as negative control. 72 hours later total RNA was extracted.

value: Monocyte-derived GM-CSF macrophages

value: siRNA GSK3A (50 nanomolar) and GSK3B (50 nanomolar)


title: Melanocytes (Hermes-4a), UVB-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_Hermes-4a_UVB_CPD

value: foreskin


title: sample 116_genomic DNA from blood sample C0628

value: normal


title: sample 115_genomic DNA from blood sample C0613

value: female


title: Melanocytes (Hermes-3a), UVB-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_Hermes-3a_UVB_CPD

value: human melanocytes, telomerase immortalized

value: Wild type


title: siRNA GSK3A+GSK3B-GM-MØ - Donor B


title: B73xMs71_DS_R3

description: Library name: 114


title: sample 114_genomic DNA from blood sample C0609


title: Melanocytes (HEM-ad), UVB-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_HEM-ad_UVB_CPD

value: Primary melanocytes (HEM-ad)

value: Primary human epidermal melanocyte (adult)


title: Melanocytes (HEM-neo), UVB-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_HEM-neo_UVB_CPD

value: Primary melanocytes (HEM-neo)

value: Primary human epidermal melanocyte (neonatal)


title: B73xNC358_WW_R1

description: Library name: 115

value: leaf blade


title: sample 113_genomic DNA from blood sample C0603


title: siRNA GSK3B-GM-MØ - Donor C

value: siRNA GSK3B (50 nanomolar)


title: Melanocytes (Hermes-4a), UVA-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_Hermes-4a_UVA_CPD

value: UVA (72 J/cm2)


title: B73xMs71_DS_R1

description: Library name: 112

value: DS


title: siRNA GSK3B-GM-MØ - Donor B


title: siRNA GSK3B-GM-MØ - Donor A


title: Melanocytes (Hermes-3a), UVA-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_Hermes-3a_UVA_CPD


title: sample 118_genomic DNA from blood sample C0668

value: major depressive disorder

value: male


title: sample 111_genomic DNA from blood sample C0556


title: Melanocytes (HEM-ad), UVA-irradiated, CPD_CD-seq (UVA vs. UVB)

description: Library name: 2_HEM-ad_UVA_CPD


title: sample 110_genomic DNA from blood sample C0518