title: PROSER1 KO+Rescue day2 in N2B27 RNA-seq biol rep 1

value: PROSER1 knockout +Rescue

value: 48 hr in N2B27


title: 176, S, day 16, biol repl 2, run 1

status: Public on Nov 20 2024

type: SRA

city: Vienna

first: Julia

last: Naas

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: 10x Genomics

library_source: transcriptomic

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

molecule: total RNA

organism: Homo sapiens

source_name: brain organoid tissue

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

tag: tissue

value: brain organoid tissue

tag: cell line

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

tag: Sex

value: female

tag: time

value: day 16

tag: treatment

value: striatum protocol (S)


title: F4_2

city: Higashihiroshima

first: Takafumi

last: Ogawa

state: Hiroshima

address: 1-3-1 Kagamiyama

country: Japan

institute: Hiroshima University

data_processing:
The annotated genes (Aligned.sortedByCoord.out.bam file from STAR outputs) were quantified using RSEM.
Assembly: Differential expression analysis of genes and transcripts was performed in R using the Bioconductor package DESeq2.
Supplementary files format and content: tab deliminated file includes raw counts.

source_name: human embryonic kidney

growth_protocol: Human embryonic kidney (HEK) 293E cells (provided by Brendan Manning) were grown in DMEM (high glucose, with L-glutamine), 10% FBS, and 1% penicillin/streptomycin supplement (all from Invitrogen).

extract_protocol:
Samples were snap-frozen in liquid nitrogen and stored at −80°C until needed. After five freeze-thaw steps in a 37°C water bath and liquid nitrogen, total RNA was extracted using TRIzol, then purified with the Direct-zol™ RNA Kit and treated with DNase I to remove possible DNA contamination.
FASTQ output files were aligned to C. elegans WBcel269 reference genomes using STAR with a 2-pass procedure.

treatment_protocol: Cells were starved by incubation in DMEM with 0.1 % FBS overnight. Re-feeding was achieved by treatment with regular growth media.

value: human embryonic kidney

value: HEK-293E cell

tag: cell type

value: embryonic kidney cells

value: 4h feeding


title: 176, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

value: day 0


title: DIPG4 ES, rep1 (RNA-seq)

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

state: CA

address: 269 Campus Drive

country: USA

institute: Stanford University

data_processing:
QC was performed with FastQC
Reads were aligned to the hg38 genome with hisat2 and indexed with samtools
transcript assembly and fpkm value calculations were performed with Cufflinks
tests for differential expression were performed with Cuffdiff
Assembly: hg38
Supplementary files format and content: tab-delimited files include FPKM values for each sample

extract_protocol:
RNA was extracted after FACS with PureLink RNA Mini kit (Invitrogen, 12183025) instructions with DNAse treatment (Invitrogen, 12185010).
Libraries were prepped following the NEBNext Ultra II Directional RNA Library Prep Kit


title: wildtype day2 in N2B27 RNA-seq biol rep 1

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

data_processing:
Adapter sequences and low-quality nucleotides were trimmed using Trimmomatic
Genome mapping performed with RNA-STAR, parameters varied between analyses; see text
Gene expression measured from mapped reads using FeatureCounts for protein coding genes or TEtranscripts for transposable elements
Differential expression in protein coding genes analysed using DESeq2
Assembly: mm10
Supplementary files format and content: Normalised counts: Tabular file generated by DESeq2 normalisation

organism: Mus musculus

source_name: differentiated embryonic stem cells

growth_protocol: DMEM high-glucose plus GlutaMAX, 8.3% ES-qualified foetal bovine serum, 4.1% knock out serum replacement, 100UI/mL Pen/strep, 0.1mM β-mercaptoethanol, 1X non-essential amino acids, 1X sodium pyruvate, 3µM GSK3 inhibitor (CHIR99021), 1µM MEK inhibitor (PD0325901), 100ng/mL LIF-GST cleaved (DU1715). Plated at 0.02x10^6 cells/mL on gelatinised plates and incubated at 37°C, 5% CO2

extract_protocol:
RNA extracted by RNeasy (QIAGEN)
Prepared using NEBNext Ultra II Directional RNA Library Prep kit (NEB)

treatment_protocol: "day 2" samples subjected to 2 day monolayer differentiation in N2B27 medium: 1:1 mix of Advanced DMEM-F12 and Neurobasal, supplemented with 1x L-Glutamine, 1x NEAA, 0.5x N-2 supplement, 0.5x B-27 supplement, and 0.1 mM β-ME

value: differentiated embryonic stem cells

tag: genotype

value: wildtype


title: S_1

value: starvation


title: wildtype day2 in N2B27 RNA-seq biol rep 2


title: 176, M, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: midbrain protocol (M)


title: DIPG4 G1, rep1 (RNA-seq)


title: LT3

data_processing:
FASTQ output files were aligned to Homo sapiens GRCh38.98 reference genomes using STAR with a 2-pass procedure.
Assembly: The annotated genes and transcripts (Aligned.sortedByCoord.out.bam file from STAR outputs) were quantified using RSEM
Supplementary files format and content: tab deliminated file includes DEG, IfcSE, and padj.

source_name: lymph node

growth_protocol: LAM cells were cultured in IIA complete media (Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12), 10% Fetal Bovine Serum (FBS), 1 nM triiodothyronine, 10 mU/mL vasopressin, 200 nM hydrocortisone, 50 nM sodium selenite, 10 nM cholesterol, 20 ng/mL EGF, 25 mg/mL insulin, 10 mg/mL transferrin, and 1.6 mM ferrous sulfate)

extract_protocol:
Total RNA was isolated using PureLink RNA Mini kit and treated with DNase I for 30 min at room temperature.
RNAseq was performed by BGI AMERICAS CORPORATION, MA. Briefly, cDNA libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit and paired-end 100 bp sequencing was performed on HiSeq 4000 (Illumina).

treatment_protocol: 80% confluent cells on 60 mm culture dishes were treated with drugs (100 nM Rapamycin, 20 μM PF4708671, 250 nM Torin1, 20 μM SRPIN340) without serum for 24 hr.

value: lymph node

value: LAM cell

value: Lymphangioleiomyomatosis

value: SRPK2KO, 3


title: 176, M, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 80


title: wildtype mESC RNA-seq biol rep 2

source_name: embryonic stem cells

value: embryonic stem cells


title: NHA G2, rep2 (RNA-seq)

source_name: NHA

value: NHA


title: DIPG4 LS, rep1 (RNA-seq)


title: LT2

value: SRPK2KO, 2


title: DIPG4 ES, rep2 (RNA-seq)


title: 176, M, day 16, biol repl 2, run 1

description: 10x Genomics

value: day 16


title: wildtype mESC RNA-seq biol rep 1


title: NHA G2, rep1 (RNA-seq)


title: S_2

value: human embryonic kidney

value: HEK-293E cell

value: embryonic kidney cells


title: DIPG4 G1, rep2 (RNA-seq)


title: PROSER1 knockout+rescue mESC EM-seq biol rep2

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using TrimGalore and mapped against the mouse genome (mm10) using Bismark (https://github.com/FelixKrueger/Bismark) with standard setting allowing for 1000bp insert size (--X 1000)
Bismark deduplicate was used to remove PCR duplicates
Bismark methylation extractor was used with the following parameter setting (--paired-end --no-overlap  --ignore_r2 3 --ignore_3prime_r2 1) to remove methylation call bias due to adaptor ligation and avoid scoring methylation calls twice in case of overlapping paired-end reads.
Methylation calls in a CpG context were merged (combining CpG methylation calls from both strands of a single CG dinucleotide) to produce a comprehensive “Methreport_CpGcomb_mm10” file containing summarised methylation calls for all CG sites in the mouse genome. These files contain with the following columns <chr><start><end><number of total reads><number of methylated reads> and can be imported directly into SeqMonk using the QasR import filter.
Assembly: mm10
Supplementary files format and content: MethReport files: Summarised methylation calls for all CG sites in the mouse genome, tabular
Library strategy: EM-seq

molecule: genomic DNA

extract_protocol:
gDNA was extracted using the Monarch Genomic DNA Purification Kit (NEB) and sheared to ~400bp using a Bioruptor Pico sonicator (Diagenode).  Libraries were prepared using the NEBNext® Enzymatic Methyl-seq Kit (NEB)
Libraries were prepared using the NEBNext® Enzymatic Methyl-seq Kit (NEB)

value: PROSER1 knockout +Rescue


title: 176, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: LS3

value: lymph node

value: LAM cell

value: SRPIN340, 3


title: LS2

value: Lymphangioleiomyomatosis

value: SRPIN340, 2


title: PROSER1 knockout+rescue mESC EM-seq biol rep1


title: NHA LS, rep1 (RNA-seq)


title: 176, D, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female


title: NHA LS, rep2 (RNA-seq)

value: NHA


title: LS1

value: SRPIN340, 1


title: PROSER1 knockout mESC EM-seq biol rep 2

value: embryonic stem cells

value: PROSER1 knockout


title: 176, D, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: NHA ES, rep2 (RNA-seq)


title: PROSER1 knockout mESC EM-seq biol rep 1


title: 176, D, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: LR3


title: 176, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: day 13


title: wildtype mESC EM-seq biol rep 2

value: wildtype


title: 176, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: DIPG4 LS, rep2 (RNA-seq)


title: LR2

value: lymph node


title: NHA G1, rep2 (RNA-seq)


title: LT1

value: LAM cell

value: SRPK2KO, 1


title: XUJA_2, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: day 120

value: ventral protocol (V)


title: LR1

value: Lymphangioleiomyomatosis


title: NHA G1, rep1 (RNA-seq)


title: NHA ES, rep1 (RNA-seq)


title: LP3

value: Torin1, 3


title: XUJA_2, V, day 80, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: female

value: day 80


title: wildtype mESC EM-seq biol rep 1

value: embryonic stem cells


title: LP2

value: Torin1, 2


title: HA-bs G2, rep2  (RNA-seq)

source_name: HA-bs

value: HA-bs


title: XUJA_2, V, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: PROSER1 knockout mESC TET2-N ChIP biol rep 3

data_processing:
Adapter sequences and low-quality nucleotides were trimmed using Trimmomatic
Genome mapping to mm10 was performed using Bowtie2 with (--very-sensitive) preset settings
Mapped reads were de-duplicated using MarkDuplicates
Mapped reads were filtered to remove those from non-chromosomal DNA, mtDNA and the Y chromosome
Peaks were called using MACS2 with paired-end settings (--format BAMPE --mfold 5 50 --bw 300 using 0.05 q-value threshold for TET2 and PROSER1 peaks and a 0.001 threshold for H3K4me1 and H3K27ac. In addition, H3K4me1 peaks were called as broad, with a broad region cutoff of 0.1
Replicate sets of peaks were merged to produce a consensus peak set using Diffbind
Bigwig files were generated from consensus peak sets or Bam files after filtering using BamCoverage from deepTools with removal of mm10 blacklisted genomic regions (--binsize 10 --normalizeUsing RPKM --extendReads --ignoreDuplicates --blackListFileName "mm10-blacklist.v2.bed.gz")
Assembly: mm10
Supplementary files format and content: BIGWIG files: genome coverage of PROSER1, TET2, H3K27ac and H3K4me1 binding/enrichment

extract_protocol:
cells were fixed with 2mM DSG for 30min followed by 1% formaldehyde for 10min. After quenching and cell lysis, the chromatin was sheared using a Bioruptor Pico sonicator (Diagenode)
The library preparation was performed using a modified Illumina TruSeq protocol. Briefly, TruSeq adaptors were ligated using NB Quick Ligase (M2200) and libraries were amplified with a KAPA HiFi Hot Start polymerase mix. After PCR amplification, size selection was performed with AMPure beads (Beckman Coulter) to obtain fragments between 250-370bp, and size distribution was validated with a Agilent Tapestation.

value: PROSER1 knockout

value: TET2-N antibody


title: PROSER1 knockout mESC TET2-N ChIP biol rep 2


title: HA-bs G2, rep1 (RNA-seq)


title: LP1

value: lymph node

value: Torin1, 1


title: XUJA_2, V, day 25, biol repl 1, run 1

description: 10x Genomics

value: day 25


title: LK3

value: LAM cell

value: rapamycin, 3


title: PROSER1 knockout mESC TET2-N ChIP biol rep 1


title: HA-bs LS, rep1 (RNA-seq)


title: wildtype mESC TET2-N ChIP biol rep 3

value: wildtype


title: LK2

value: Lymphangioleiomyomatosis

value: rapamycin, 2


title: XUJA_2, S, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: day 120

value: striatum protocol (S)


title: HA-bs ES, rep2 (RNA-seq)


title: wildtype mESC TET2-N ChIP biol rep 2

value: embryonic stem cells


title: XUJA_2, S, day 80, biol repl 1, run 1

description: 10x Genomics

value: female

value: day 80


title: wildtype mESC ChIP input

value: input


title: HA-bs ES, rep1 (RNA-seq)

value: HA-bs


title: LK1

value: lymph node

value: rapamycin, 1


title: wildtype mESC TET2-N ChIP biol rep 1

value: TET2-N antibody


title: LF3

value: LAM cell


title: HA-bs G1, rep2 (RNA-seq)


title: XUJA_2, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16


title: HA-bs G1, rep1 (RNA-seq)


title: LF1


title: LD3

value: control, 3


title: LF2

value: Lymphangioleiomyomatosis


title: PROSER1 knockout mESC H3K4me1 ChIP biol rep 2

value: PROSER1 knockout

value: H3K4me1 antibody (AB_10695148)


title: XUJA_2, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: midbrain protocol (M)


title: PROSER1 knockout mESC H3K4me1 ChIP biol rep 3

value: embryonic stem cells


title: DIPG33 S4, rep2 (Repli-seq)

data_processing:
Repli-seq reads in each of the surveyed cell cycle phases (S1, S2, S3, S4) were mapped to hg19 reference genome
removal of duplicates and counting reads over a 50 Kb bins across the genome
counts were then quantile normalized and LOESS smoothed
Assembly: hg19
Supplementary files format and content: wig files with normalized counts
Library strategy: Repli-seq

extract_protocol:
Cells were then treated with proteinase K and DNA was extracted following the Zymo Quick-DNA Microprep Kit extraction instructions (Zymo Research, D3020). DNA was sonicated using a QSonica Q700 (10 min at 20% amplitude).
Libraries were constructed using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs, E7370L)

tag: chip antibody

value: Brdu (BD pharmigen, cat. 555627)


title: DIPG33 S4, rep1 (Repli-seq)


title: PROSER1 knockout mESC H3K4me1 ChIP biol rep 1


title: wildtype mESC H3K4me1 ChIP biol rep 3

value: wildtype


title: XUJA_2, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: female

value: day 13

value: ventral protocol (V)


title: DIPG33 S3, rep2 (Repli-seq)


title: LD2

value: lymph node

value: control, 2


title: XUJA_2, S, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40

value: striatum protocol (S)


title: XUJA_2, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: wildtype mESC H3K4me1 ChIP biol rep 2


title: LD1

value: LAM cell

value: Lymphangioleiomyomatosis

value: control, 1


title: XUJA_2, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 0


title: wildtype mESC H3K4me1 ChIP biol rep 1

value: H3K4me1 antibody (AB_10695148)


title: MOLM13_sgPCGF1_8_VTP50469_Rep2

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

data_processing:
The paired-end reads were mapped to the human genome (hg38) using STAR (v2.5.1b) with default parameters.
Assembly: hg38
Supplementary files format and content: csv, normalized counts

source_name: cell line

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen, Germany).
RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s protocol. The quality and concertation of the libraries were examined by Bioanalyzer High Sensitivity DNA Chip (Agilent). The multiplexed RNA-Seq libraries were paired-end sequenced for 150 bp on the Illumina HiSeq 4000 platform.

treatment_protocol: Cells were lentivirally infected with indicated sgRNA for gene knockout. Cells were treated with DMSO or 1µM VTP50469 for 6 days.

value: cell line

value: Acute myeloid leukemia cells

value: PCGF1 knockout


title: DIPG33 S2, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: DIPG33 S3, rep1 (Repli-seq)


title: XUJA_2, M, day 16, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: female

value: day 16

value: midbrain protocol (M)


title: XUJA_2, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: XUJA_2, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: XUJA_2, D, day 40, biol repl 1, run 1

description: 10x Genomics


title: MOLM13_sgPCGF1_8_VTP50469_Rep1


title: DIPG33 S2, rep1 (Repli-seq)


title: PROSER1 knockout mESC H3K27ac ChIP biol rep 3

value: embryonic stem cells

value: PROSER1 knockout

value: H3K27ac antibody (AB_2608307)


title: PROSER1 knockout mESC H3K27ac ChIP biol rep 1


title: DIPG33, S1, rep2 (Repli-seq)


title: MOLM13_sgPCGF1_8_DMSO_Rep1

value: DMSO


title: DIPG33, S1, rep1 (Repli-seq)


title: PROSER1 knockout mESC H3K27ac ChIP biol rep 2


title: DIPG29 S4, rep2 (Repli-seq)


title: MOLM13_sgLuc_VTP50469_Rep2

value: Wildtype


title: XUJA_2, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 13


title: wildtype mESC H3K27ac ChIP biol rep 3

value: wildtype


title: MOLM13_sgLuc_VTP50469_Rep1

value: cell line

value: Acute myeloid leukemia cells


title: DIPG29 S4, rep1 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: ROZH_5, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: female

value: ventral protocol (V)


title: XUJA_2, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: day 25


title: DIPG29 S3, rep2 (Repli-seq)


title: HA-bs LS, rep2 (RNA-seq)

value: HA-bs


title: ROZH_5, V, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: MOLM13_sgPCGF1_8_DMSO_Rep2

value: PCGF1 knockout


title: wildtype mESC H3K27ac ChIP biol rep 1

value: embryonic stem cells

value: H3K27ac antibody (AB_2608307)


title: PROSER1 knockout mESC PROSER1-N ChIP biol rep 2

value: PROSER1 knockout

value: PROSER1-N antibody


title: DIPG29 S3, rep1 (Repli-seq)


title: MOLM13_sgLuc_DMSO_Rep1

value: Wildtype

value: DMSO


title: ROZH_5, V, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 40


title: PROSER1 knockout mESC PROSER1-N ChIP biol rep 1


title: ROZH_5, V, day 25, biol repl 1, run 1

description: 10x Genomics


title: wildtype mESC PROSER1-N ChIP biol rep 2

value: wildtype


title: DIPG29 S2, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: MV411_sgPCGF1_8_VTP50469_Rep2

value: cell line

value: Acute myeloid leukemia cells


title: DIPG29, S1, rep2 (Repli-seq)


title: MV411_sgPCGF1_8_DMSO_Rep1


title: MV411_sgPCGF1_8_VTP50469_Rep1


title: ROZH_5, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: female

value: day 13

value: ventral protocol (V)


title: DIPG29, S1, rep1 (Repli-seq)


title: DIPG29 S2, rep1 (Repli-seq)


title: ROZH_5, S, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80

value: striatum protocol (S)


title: MV411_sgPCGF1_8_DMSO_Rep2

value: PCGF1 knockout


title: Isotype 5 Retina

city: Philadelphia

first: Jessica

last: McCord

state: PA

institute: Thomas Jefferson University

data_processing:
Hisat2 v2.0.5 and featrueCounts v1.5.0-p3
Raw data was cleaned by removing reads containing adaptor, reads containing poly-N and low quality reads.
Index of the reference genome was built using Hisat2 and clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featrueCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Retina

extract_protocol:
RNA was harvested using Rnaesy mini plus kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: mice were treated with anti CXCR3 andtibody (25ug/g) or irrelavent control antibody on day 0, 5, and 10 post natal dat=y

value: Retina

value: BALB/c

value: Day 15

value: Irrelavent antibody


title: MOLM13_sgLuc_DMSO_Rep2

value: Wildtype

value: DMSO


title: wildtype mESC H3K27ac ChIP biol rep 2

value: embryonic stem cells

value: wildtype

value: H3K27ac antibody (AB_2608307)


title: wildtype mESC PROSER1-N ChIP biol rep 1

value: PROSER1-N antibody


title: MV411_sgLuc_VTP50469_Rep2

value: cell line

value: Acute myeloid leukemia cells


title: ROZH_5, S, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: female

value: day 40


title: DIPG24 S4, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: Isotype 4 RPE

source_name: RPE/Choroid

value: RPE/Choroid


title: ROZH_5, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16

value: striatum protocol (S)


title: DIPG24 S4, rep1 (Repli-seq)


title: Isotype 4 Retina

value: Retina

value: BALB/c

value: Day 15

value: Irrelavent antibody


title: MV411_sgLuc_DMSO_Rep2

value: Wildtype

value: DMSO


title: DIPG24 S3, rep2 (Repli-seq)


title: ROZH_5, S, day 120, biol repl 1, run 1

description: 10x Genomics

value: day 120


title: MV411_sgLuc_DMSO_Rep1

value: cell line


title: ROZH_5, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

value: day 0


title: Isotype 5 RPE


title: Isotype 3 RPE


title: ROZH_5, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: midbrain protocol (M)


title: DIPG24 S3, rep1 (Repli-seq)


title: AML2_sgBCOR_7_VTP50469_Rep2

value: Acute myeloid leukemia cells

value: BCOR knockout


title: ROZH_5, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: female

value: day 80


title: Isotype 3 Retina


title: Isotype 2 RPE

value: RPE/Choroid


title: DIPG24 S2, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: DIPG24 S2, rep1 (Repli-seq)


title: AML2_sgBCOR_7_DMSO_Rep2


title: DIPG24, S1, rep2 (Repli-seq)


title: ROZH_5, M, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16


title: AML2_sgBCOR_7_VTP50469_Rep1


title: Isotype 1 RPE

value: BALB/c

value: Day 15


title: MV411_sgLuc_VTP50469_Rep1

value: Wildtype


title: DIPG24, S1, rep1 (Repli-seq)


title: ROZH_5, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: dorsal protocol (D)


title: AML2_sgPCGF1_8_VTP50469_Rep2

value: PCGF1 knockout


title: ROZH_5, D, day 80, biol repl 1, run 1

description: 10x Genomics


title: DIPG21 S4, rep2 (Repli-seq)


title: DIPG21 S4, rep1 (Repli-seq)


title: Isotype 1 Retina

value: Retina

value: Irrelavent antibody


title: DIPG21 S3, rep2 (Repli-seq)


title: ROZH_5, D, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 40


title: ROZH_5, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: day 25


title: CXCR3 5 RPE

value: anti CXCR3


title: CXCR3 4 RPE


title: ROZH_5, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: midbrain protocol (M)


title: AML2_sgPCGF1_8_DMSO_Rep1

value: cell line

value: Acute myeloid leukemia cells

value: DMSO


title: DIPG21 S3, rep1 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: ROZH_5, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: female

value: day 13


title: AML2_sgPCGF1_8_DMSO_Rep2


title: H9, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: day 120

value: ventral protocol (V)


title: CXCR3 5 Retina

value: Retina

value: BALB/c

value: Day 15


title: DIPG21 S2, rep2 (Repli-seq)


title: AML2_sgLuc_VTP50469_Rep2

value: Wildtype


title: CXCR3 3 RPE

value: RPE/Choroid


title: CXCR3 4 Retina

value: anti CXCR3


title: AML2_sgLuc_VTP50469_Rep1


title: Isotype 2 Retina

value: Irrelavent antibody


title: AML2_sgPCGF1_8_VTP50469_Rep1

value: PCGF1 knockout


title: DIPG21 S1, rep2 (Repli-seq)


title: AML2_sgBCOR_7_DMSO_Rep1

value: cell line

value: BCOR knockout


title: CXCR3 3 Retina


title: H9, V, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 40


title: AML2_sgLuc_DMSO_control_Rep2

value: Acute myeloid leukemia cells

value: DMSO


title: DIPG21 S2, rep1 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: DIPG21 S1, rep1 (Repli-seq)


title: CXCR3 2 RPE


title: CXCR3 2 Retina


title: AML2_sgLuc_DMSO_control_Rep1


title: H9, V, day 25, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female

value: day 25


title: DIPG19 S4, rep2 (Repli-seq)


title: H9, S, day 120, biol repl 1, run 1

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: DIPG19 S4, rep1 (Repli-seq)


title: gnrh3 knockout, scRNAseq

first: Sakura

last: Tanaka

address: 1201 Welch Road

library_source: transcriptomic single cell

data_processing:
Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software.
Quality control, normalization, data integration, and clustering were performed using Seurat v4 R package.
Assembly: GRCz11/danRer11
Supplementary files format and content: Tab-separated values files, matrix file, and comma-separated values file

organism: Danio rerio

source_name: Pituitary

extract_protocol:
Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate-buffered saline (PBS) and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander-Cohen et al (2021) and Fabian et al (2020) with some modifications. Briefly, the samples were centrifuged at 2,000 × rpm for 5 minutes at 4°C, then PBS was removed followed by a treatment of dissociation solution (0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter) at 28.5°C for 40 minutes, with gently pipetting every 10 minutes using a wide bore tip. After incubation, the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum (FBS) in PBS] and gently mixed it by pipetting, followed by centrifuging at 2,000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded, then 1 mL Accumax working solution (30% Accumax in PBS) was added, and the cells were gently resuspended. After incubation at room temperature for 5 minutes, the dissociated cells were filtered through 40 µm pore cell strainer. After centrifuging at 2,000 × rpm for 5 minutes at 4°C, the supernatant was removed, and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing.
cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4,000 cells per sample.

value: Pituitary

tag: age

value: Adult 3-month-old


title: CXCR3 1 RPE

value: RPE/Choroid

value: BALB/c

value: Day 15

value: anti CXCR3


title: WT, scRNAseq

value: wild-type


title: H9, S, day 80, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: H9, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: day 13

value: ventral protocol (V)


title: CXCR3 1 Retina

value: Retina


title: Control 5 RPE

value: Control


title: DIPG19 S3, rep1 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: metVali2_PPshunt_lib2

city: Worcester

first: Xuhang

last: Li

state: Massachusetts

address: 55 N Lake Ave

department: Department of Systems Biology

institute: University of Massachusetts Medical School

description: Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains 50 samples for biological triplicate of a series of RNAi knockdowns and metabolite supplementation treatments. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline.

data_processing:
As part of the WPS data processing pipeline, raw reads were processed using an in-house dolphinNext pipeline to generate a gene-by-sample read count matrix.
Raw reads were demultiplexed by a homemade python script that extracts the barcode information from read 1 and combines that with read 2.
The processed reads were passed to Trimmomatic (v0.32) to remove polyA and adaptor sequences.
Next, reads were aligned to the C. elegans genome (WormBase WS279) by STAR (parameter: --runThreadN 4 --alignIntronMax 25000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Finally, the output bam file was processed by ESAT to obtain the read counts of genes. In ESAT, we used an extension window of 1000 bp and the ‘proper’ method of multiple mappings. Unique Molecular Identifier (UMI) features were not used by setting umiMin = 1. Read counts, rather than UMI counts, were used as the gene expression quantity. We did not observe significant PCR duplicates during the development of our method (i.e., read counts highly correlate with UMI counts, data not shown), which is consistent with the low number of PCR cycles for library construction. Therefore, we directly used the read counts regardless of the presence of UMI in our library.
Assembly: WormBase WS279
Supplementary files format and content: a comma-separated values (CSV) file for the gene-by-sample read count matrix
Supplementary files format and content: a comma-separated values (CSV) file detailed annotation of sample barcode and sample information for all libraries included here

organism: Caenorhabditis elegans

source_name: WPS multiplexed RNA-seq library - gene knockdowns related to propionate breakdown metabolism under various B12 concentration - lib2

growth_protocol: The N2 strain was used as the wild-type strain. Animals were maintained at 20°C on nematode growth media (NGM) and fed with E. coli HT115 containing the empty RNAi vector L4440. In RNAi experiments, animals were fed with the RNAi bacteria from first larval (L1) stage, followed by incubation at 20°C for approximately 63 hours to collect gravid adults. To prepare PFA-killed HT115 diet, we followed established protocols as described previously (Safa Beydoun,Communications Biology, 2021). The animals fed on PFA-killed HT115 developed slightly slower, therefore were harvested at 65 hours post L1.

extract_protocol:
Animals were transferred to 96-well plates for high-throughput RNA extraction following protocol described in the WPS method paper. Importantly, this method only extracts total RNA from adult animal tissues and leaves any eggs intact.
Extracted total RNA was barcoded during reverse transcription to enable early pooling of samples. Multiplexed RNA-seq libraries each containing ~50 samples were constructed following a protocol adapted from the CEL-seq2 single-cell RNA-seq library construction method (Hashimshony, Genome Biology, 2016). For detailed protocols, refer to our WPS method paper. This library construction method produces a multiplexed RNA-seq library comprising ~50 samples.

treatment_protocol: RNAi treatments were performed by feeding HT115 bacteria expressing corresponding dsRNA, as stated in "growth protocol". Double knockdowns were performed using newly constructed RNAi clones that expressed a dsRNA covering both targeted genes, each with ~500bp fragment aligned to the targeted gene's protein coding region. Feeding C. elegans with bacteria expressing double RNAi in one plasmid was shown to have higher knockdown efficiency than feeding a mixture of bacteria that each expressed a single dsRNA species (Kyoengwoo Min, Biotechniques, 2010). Metabolite supplementation was achieved through supplementing metabolites in the NGM plate with final concentrations labeled in corresponding metadata information column.

value: Whole animal (excluding eggs)

tag: strain

tag: developmental stage

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including vector control (L4440) RNAi and RNAi knockdowns of two genes in propionate canonical (pccb-1 and mmcm-1) and two genes in shunt (acdh-1 and hphd-1) degradation pathways, under a gradient of vitamin B12 supplementation (0, 1, 4, 16nM).


title: DIPG19 S3, rep2 (Repli-seq)


title: metVali2_PPshunt_lib1

description: Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains 48 samples for biological triplicate of a series of RNAi knockdowns and metabolite supplementation treatments. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline.

source_name: WPS multiplexed RNA-seq library - gene knockdowns related to propionate breakdown metabolism under various B12 concentration - lib1

value: Including vector control (L4440) RNAi and RNAi knockdowns of two genes in propionate canonical (pccb-1 and mmcm-1) and two genes in shunt (acdh-1 and hphd-1) degradation pathways, under a gradient of vitamin B12 supplementation (0, 0.0625, 0.25nM).


title: H9, S, day 40, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female

value: day 40

value: striatum protocol (S)


title: H9, V, day 80, biol repl 1, run 1

description: 10x Genomics


title: Control 5 Retina

value: BALB/c

value: Day 15


title: Control 4 RPE

value: RPE/Choroid


title: Metabolic gene WPS series met9-lib6

description: Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains the triplicate samples for ~16 RNAi conditions targeting different metabolic genes and six samples from empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline.

source_name: Whole animal (excluding eggs)

growth_protocol: The N2 strain was used as the wild-type strain. Animals were maintained at 20°C on nematode growth media (NGM) and fed with E. coli HT115 containing the empty RNAi vector L4440. In WPS experiments, animals were fed with the RNAi bacteria from first larval (L1) stage, followed by incubation at 20°C for approximately 63 hours to collect gravid adults. In cases where RNAi feeding led to developmental delays, synchronized L1 animals were initially fed with vector control RNAi-containing bacteria and animals were transferred to the corresponding RNAi plates at 17 hours (L2 stage) or 25 hours post-plating (L3 stage) to circumvent RNAi-associated developmental delays. By delayed RNAi exposure, animals typically developed to gravid adult stage at similar stage as control. The supplementary metadata table includes condition-specific growth information (i.e., seeding stages).

extract_protocol:
Animals were transferred to 96-well plates for high-throughput RNA extraction following protocol described in the WPS method paper. Importantly, this method only extracts total RNA from adult animal tissues and leaves any eggs intact.
Extracted total RNA was barcoded during reverse transcription to enable early pooling of samples. Multiplexed RNA-seq libraries each containing ~50 samples were constructed following a protocol adapted from the CEL-seq2 single-cell RNA-seq library construction method (Hashimshony, Genome Biology, 2016). For detailed protocols, refer to our WPS method paper. This library construction method produces a multiplexed RNA-seq library comprising triplicates of 15-16 conditions and six independent vector controls.

treatment_protocol: See "growth protocol".

value: Including empty vector controls and single gene RNAi knockdown for genes:vha-6, hrg-4, swd-2.2, ceeh-2, moc-5, acl-4, hpo-19, dyn-1, cox-6C, T27A8.2, rpc-11, cyp-37A1, acox-3, fmo-1, C27D8.4, acox-1.5.


title: DIPG19 S2, rep2 (Repli-seq)


title: Metabolic gene WPS series met9-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:sams-1, eppl-1, rpb-12, C34C6.4, ogdh-1, wac-1.1, plpp-1.1, mars-1, hars-1, F19B6.1, cah-1, T07D4.2, C10C5.5, cyp-35A2, png-1, T20B3.1.


title: H9, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 0


title: H9, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16


title: Control 4 Retina

value: Retina

value: Control


title: Metabolic gene WPS series met9-lib4

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:dut-1, nkb-3, acox-1.3, nyn-2, spr-5, gbh-2, ucp-4, dhs-28, cox-7C, let-754, polg-1, C24A3.4, linc-169, W10C8.5, Y39G8B.2, VECTORLIKE-cbp-1.


title: DIPG19, S1, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: DIPG19 S2, rep1 (Repli-seq)


title: H9, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female

value: day 120

value: midbrain protocol (M)


title: Control 3 RPE

value: RPE/Choroid

value: BALB/c

value: Day 15


title: DIPG19, S1, rep1 (Repli-seq)


title: H9, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: H9, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: DIPG4 S4, rep2 (Repli-seq)


title: H9, M, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16


title: Metabolic gene WPS series met9-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:hrg-1, T25B9.8, mys-2, C13C4.4, spe-5, sir-2.2, fce-1, F58F12.1, C34B2.8, pole-2, aco-2, cts-1, set-1, ppt-1, F48E3.9, nhr-38.


title: H9, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: dorsal protocol (D)


title: DIPG4 S4, rep1 (Repli-seq)


title: Control 2 Retina

value: Retina

value: Control


title: Metabolic gene WPS series met8-lib6

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:pnk-1, SHORT-C15H9.5, pho-5, egl-8, flad-1, F35C8.5, Y97E10AR.2, Y41D4A.6, gpx-5, C31H2.4, algn-10, coq-2, C27A7.1, Y7A9A.1, C27A7.3, acp-1.


title: DIPG4 S3, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: Control 1 RPE


title: H9, D, day 80, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female


title: DIPG4 S3, rep1 (Repli-seq)


title: H9, D, day 40, biol repl 1, run 1

description: 10x Genomics


title: Metabolic gene WPS series met8-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:gpx-7, gpx-2, VECTORLIKE-aman-2, mtm-1, F26C11.1, gpx-1, T05H4.4, VECTORLIKE-H14N18.4, R10H10.6, pho-7, sod-5, sod-1, Y94H6A.10, nprt-1, Y38F2AR.12.


title: Control 1 Retina

value: BALB/c

value: Day 15


title: DIPG4 S2, rep2 (Repli-seq)


title: Metabolic gene WPS series met8-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:sod-2, T05G5.5, lfe-2, gss-1, clk-1, gpx-4, qns-1, SHORT-F53A10.2, Y71H2AM.6, gcs-1, sod-3, anmt-3, drr-2, algn-6, pigq-1, pho-8.


title: Metabolic gene WPS series met8-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:cchl-1, nmat-2, cyp-32A1, gsr-1, ppk-3, MULTIPLE-acp-3-4, cox-10, pho-14, tpk-1, T19H12.6, nhr-50, SHORT-let-268, nmat-1, SHORT-xpo-1, C27A2.12, SHORT-acp-2.


title: Metabolic gene WPS series met9-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:set-32, F02D8.4, mys-1, sup-18, adsl-1, piki-1, SHORT-folt-2, rpoa-12, adss-1, cdt-1, set-12, SHORT-figo-1, nmrk-1, F58A6.1, C39B5.6.


title: H9, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 25


title: Infected D28 3

source_name: Eye

value: Eye

value: Day 28

value: Infected


title: Control 3 Retina

value: Retina

value: Control


title: DIPG4 S1, rep2 (Repli-seq)


title: DIPG4 S2, rep1 (Repli-seq)


title: Metabolic gene WPS series met9-lib2

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:set-2, rnr-2, plc-1, fgt-1, R53.4, R04F11.2, ltah-1.2, aass-1, gdh-1, cpt-6, SHORT-bli-4, fmo-5, moc-1, elpc-3, VECTORLIKE-rpom-1.


title: H9, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female

value: day 13

value: dorsal protocol (D)


title: Control 2 RPE

value: RPE/Choroid

value: BALB/c

value: Day 15


title: Metabolic gene WPS series met8-lib2

value: Including empty vector controls and single gene RNAi knockdown for genes:uda-1, F02E9.7, piga-1, pdxk-1, pho-11, E01A2.1, gpx-3, SHORT-sod-4, tag-307, anmt-1, cest-5.1, icmt-1, VECTORLIKE-ZC434.8, C53D5.5, T03D8.6, pho-4.


title: H1, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 120

value: ventral protocol (V)


title: Infected D28 1

value: Eye

value: Day 28

value: Infected


title: DIPG4 S1, rep1 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: H1, V, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: Metabolic gene WPS series met7-lib6

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:pck-2, div-1, hxk-2, pgk-1, gpd-3, W06E11.1, hxk-3, F53F4.13, pfkb-1.1, Y57G11C.3, D2096.12, gob-1, RCBVECTOR-R151.2, bgal-2, T21C9.6, MULTIPLE-chil-19-21.


title: NHA S4, rep2 (Repli-seq)

value: NHA


title: Infected D15 2

value: Day 15


title: Metabolic gene WPS series met8-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:coq-6, hpd-1, prdx-3, exc-15, F25H9.6, ptps-1, C44B7.7, gpx-8, cox-15, RCBVECTOR-nnt-1, NOSIGNAL-moc-3, nit-1, SHORT-acs-6, trxr-2, ctl-2.


title: Infected D15 3


title: H1, V, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 40


title: Metabolic gene WPS series met7-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:gpi-1, R04B5.5, adh-5, Y43F4B.5, tre-1, acs-19, bre-1, alh-12, pgph-2, tre-4, aagr-2, agl-1, bgal-1, F41E6.5, VECTORLIKE-F26D11.1, pfk-1.2.


title: NHA S4, rep1 (Repli-seq)


title: Infected D10 3

value: Day 10


title: H1, V, day 25, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 25

value: ventral protocol (V)


title: Metabolic gene WPS series met7-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:hxk-1, MULTIPLE-col-166-167-168-169-170, sodh-1, T22F3.2, Y105E8B.9, him-14, alh-1, T04A8.7, tps-2, ger-1, gana-1, R05F9.6, men-1, alh-5, Y71F9B.9, icl-1.


title: NHA S3, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: NHA S3, rep1 (Repli-seq)


title: Infected D28 2

value: Eye

value: Day 28

value: Infected


title: Metabolic gene WPS series met7-lib3

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:pck-1, ipgm-1, gyg-2, tre-2, ZK632.4, dlat-2, pfkb-1.2, tpi-1, Y47D9A.1, F07A11.5, C50D2.7, gale-1, pck-3, polg-1, SHORT-gsy-1, pgph-3.


title: H1, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 13


title: Infected D15 1

value: Day 15


title: Infected D10 2

value: Day 10


title: H1, S, day 80, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: day 80

value: striatum protocol (S)


title: NHA S2, rep2 (Repli-seq)

value: NHA


title: Metabolic gene WPS series met7-lib2

value: Including empty vector controls and single gene RNAi knockdown for genes:alh-9, tkt-1, rpia-1, Y39G8B.1, aldo-1, cha-1, K08E3.5, gpd-4, tald-1, alh-4, ipgm-1, gspd-1, pyk-2, ZK1058.3, Y17G7B.3.


title: H1, S, day 120, biol repl 1, run 1

description: 10x Genomics

value: male

value: day 120


title: H1, S, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: NHA S1, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: Infected D10 1

value: Eye

value: Infected


title: Infected D5 2

value: Day 5


title: Metabolic gene WPS series met6-lib5

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:met-2, sdhb-1, MULTIPLE-pars-2-T27F6.6, crls-1, C18E9.4, dyb-1, qars-1, nuo-3, nfs-1, unc-26, bca-1, C16A3.5, lpd-5, Y51H1A.3, ZK809.3, R07E4.3.


title: NHA S2, rep1 (Repli-seq)


title: H1, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 16


title: Metabolic gene WPS series met7-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:alh-11, enol-1, C46C2.5, fbp-1, klo-2, D2063.1, aldo-2, MULTIPLE-gpd-1-2-3-4, pyk-1, tps-1, klo-1, gpd-2, gyg-1, shpk-1, R02D5.3.


title: Infected D5 1


title: H1, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: day 0


title: Infected D5 3


title: Metabolic gene WPS series met6-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:nduf-5, asg-1, C25H3.11, M01E11.1, Y63D3A.7, nuo-2, R01H10.7, cat-4, asg-2, cyc-2.2, sdha-1, F45H10.2, K08C9.1, coq-1, VECTORLIKE-jhdm-1.


title: HA-bs S4, rep1 (Repli-seq)

value: HA-bs


title: HA-bs S4, rep2  (Repli-seq)


title: Control D28 1

value: Day 28

value: Control


title: HA-bs S3, rep2 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: Metabolic gene WPS series met6-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:nuo-6, nuo-5, Y56A3A.19, VECTORLIKE-F53F4.10, mvk-1, plc-4, ldh-1, set-4, cyc-1, T02H6.11, gas-1, mmab-1, VECTORLIKE-idi-1, algn-12, RCBVECTOR-atp-3, F21C3.6.


title: H1, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: male

value: day 120

value: midbrain protocol (M)


title: H1, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: Control D28 2

value: Eye


title: H1, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: Control D15 3

value: Day 15


title: Metabolic gene WPS series met6-lib6

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:RCBVECTOR-hpo-18, F59C6.5, mev-1, rars-2, acs-22, cyc-2.1, let-721, gln-5, ttx-7, maoc-1, F44G4.2, ucr-2.2, ucr-2.1, D2030.4, srg-32, RCBVECTOR-T26E3.7.


title: Metabolic gene WPS series met6-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:nuo-1, T20H4.5, sdha-2, mes-2, prx-10, rsp-8, F42G8.10, F09E5.3, dif-1, aap-1, ucr-2.3, F45H10.3, nduf-2.2, asp-1, F31D4.9.


title: HA-bs S3, rep1 (Repli-seq)

value: HA-bs


title: HA-bs S2, rep2 (Repli-seq)


title: Metabolic gene WPS series met5-lib6

value: Including empty vector controls and single gene RNAi knockdown for genes:acly-2, algn-9, sucg-1, fntb-1, age-1, pcaf-1, Y76A2B.5, mtrr-1, idh-1, T20B12.7, F11G11.5, mpst-3, cysl-4, SHORT-metr-1, mpst-2.


title: Control D15 2

value: Control


title: H1, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: dorsal protocol (D)


title: Metabolic gene WPS series met5-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:cbs-1, idh-2, vha-7, ahcy-1, RCBVECTOR-pri-1, tir-1, daf-41, inos-1, mthf-1, T25D3.3, mel-32, mpst-1, SHORT-alh-3, mpst-7, cbs-2.


title: HA-bs S2, rep1 (Repli-seq)

value: Brdu (BD pharmigen, cat. 555627)


title: H1, D, day 80, biol repl 1, run 1

description: 10x Genomics

value: male


title: NHA S1, rep1 (Repli-seq)

value: NHA


title: HA-bs S1, rep2 (Repli-seq)


title: Metabolic gene WPS series met5-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:pps-1, got-2.2, fnta-1, rpb-6, sucl-1, unc-32, F53F1.2, qdpr-1, cbl-1, got-2.1, cysl-3, sams-4, aps-2, sucl-2, gcsh-2.


title: Control D28 3

value: Eye

value: Day 28


title: Metabolic gene WPS series met5-lib3

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:sams-5, idhg-2, bpnt-1, pdi-1, kars-1, atic-1, dhfr-1, hrde-4, ppk-2, tyms-1, F48E8.3, acly-1, suca-1, npr-32, mpst-4.


title: H1, D, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: Control D10 2

value: Day 10


title: Metabolic gene WPS series met5-lib2

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:ZK973.11, ttc-4, dhs-25, sams-3, snx-1, got-1.2, rpb-11, VECTORLIKE-F13B12.4, F21G4.1, cdo-1, F25B5.6, str-7, SHORT-mtm-3, gcsh-1.


title: Metabolic gene WPS series met6-lib2

value: Including empty vector controls and single gene RNAi knockdown for genes:F37C12.3, C33A12.1, algn-2, Y48E1B.3, asb-1, sdhd-1, Y71H2AM.4, T27E9.2, nduf-6, nuo-4, nduf-9, RCBVECTOR-atp-5, ocrl-1, cah-3, SHORT-fdps-1, SHORT-F27D4.1.


title: Control D10 3

value: Control


title: Sensory neurons from FD iPSC S3 treated with genipin, day 20, biol rep 4

city: Athens

first: Nadja

last: Zeltner

state: GA

address: 325 Riverbend Road

institute: University of Georgia

data_processing:
Analyses were done on the Galaxy platform (www.usegalaxy.org)
Low quality bases were trimmed using Trimmomatic (version 0.38)
Reads were mapped to the human genome using HISAT2 (version 2.2.1)
Reads per gene were counted using HTSeq (version 0.9.1). Minimum alignment quality value of 10
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts per gene

molecule: polyA RNA

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and purified following the manufacturer's protocol
Library was prepared using the kit NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) following the standard protocol

value: iPSC

value: FD

value: genipin (10 microM)


title: H1, M, day 16, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 16

value: midbrain protocol (M)


title: Control D10 1

value: Eye


title: H1, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: day 25

value: dorsal protocol (D)


title: Sensory neurons from FD iPSC S3 treated with genipin, day 20, biol rep 3


title: Metabolic gene WPS series met5-lib1

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:cth-2, dlst-1, pigc-1, msra-1, C06A6.4, ethe-1, K07E3.4, dpy-11, dao-3, gcst-1, idhb-1, VECTORLIKE-folt-1, unc-25, F38B6.3.


title: Control D5 3

value: Day 5


title: H1, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: day 13


title: Control D15 1

value: Day 15

value: Control


title: Control D5 2


title: Sensory neurons from FD iPSC S3 treated with genipin, day 20, biol rep 2

value: iPSC

value: FD


title: 178, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: day 120

value: ventral protocol (V)


title: 178, V, day 80, biol repl 1, run 1

description: 10x Genomics

value: male

value: day 80


title: Metabolic gene WPS series met4-lib5

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:pdi-2, SHORT-Y71H10B.1, ndk-1, nduf-6, pyc-1, aman-3, C01G6.5, cdd-2, pyr-1, guk-1, acl-14, cdd-1, bus-18, pamn-1.


title: Metabolic gene WPS series met4-lib6

value: Whole animal (excluding eggs)

value: Including empty vector controls and single gene RNAi knockdown for genes:set-14, B0001.4, F25B5.3, vha-18, C23H5.8, ZK643.2, gcy-23, cah-4, pfas-1, NOSIGNAL-dgat-2, hprt-1, dhp-2, ndx-2, Y50E8A.6.


title: Metabolic gene WPS series met4-lib4

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:umps-1, pges-2, uda-1, T22D1.3, ftn-2, upb-1, B0491.7, spl-2, NOSIGNAL-pisy-1, dtmk-1, F38B2.4, F32D1.5, VECTORLIKE-acy-1.


title: Control D5 1

value: Eye

value: Day 5


title: 178, V, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: HA-bs S1, rep1 (Repli-seq)

value: HA-bs

value: Brdu (BD pharmigen, cat. 555627)


title: Sensory neurons from FD iPSC S3, day 20, biol rep 4

value: iPSC

value: FD


title: Metabolic gene WPS series met4-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:hap-1, SHORT-lars-1, C47B2.2, MULTIPLE-acl-9-unknown, daf-18, ampd-1, thk-1, C07D8.6, xdh-1, apy-1, gcy-12, ndx-6, SHORT-F58F9.1, pde-1.


title: dorsal root ganglia, AEW, rep2

city: Shanghai

first: Li

last: Liu

state: Please select...

address: Shanghai Pudong New Area Renji Hospital

country: China

institute: shanghai jiaotong university

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dorsal root ganglia

extract_protocol:
L4-5 DRGs from adult mice (8 weeks) were collected in cold complete saline solution (CSS, 137 mM NaCl, 5.3 mM KCl, MgCl2-6H2O, 25 mM Sorbitol, 10 mM HEPES, 3 mM CaCl2, pH=7.2) and then incubated in an enzyme solution in CSS composed of 0.35 U/ml Liberase TM (Roche) and 0.6 mM EDTA TM 37 °C for 20 minutes, followed by incubation at 37°C for 10min in CSS composed of 0.35 U/ml Liberase TL (Roche), 0.6 mM EDTA, and 30 U/ml papain (Worthington Biochemical). Enzymatic digestion was stopped by adding 1ml of DRG media supplemented with 1.5 mg/ml bovin serum albumin (BSA, Sigma) and 1.5 mg/ml trypsin inhibitor (Sigma). After gentle trituration with 1 ml pipette, DRG neurons were centrifuged at 800rpm for 2-3 min and resuspended in 1 ml DH10 solution (90% DMEM/F-12, 10% FBS, 100 U/ml penicillin, and 100 μg/ml Streptomycin, Gibco).
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: dorsal root ganglia

value: Neuron

value: wildtype

value: acetone-ether-water-treated group


title: Sensory neurons from FD iPSC S3, day 20, biol rep 3


title: 178, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 13

value: ventral protocol (V)


title: Metabolic gene WPS series met4-lib2

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:dhod-1, F40F8.1, MULTIPLE-nhr-76-lin-7, VECTORLIKE-gcy-18, adah-1, pdi-3, drp-1, R12E2.11, pde-2, adal-1, dhp-1, K05B2.4, acy-2, hosl-1, pde-4.


title: Sensory neurons from FD iPSC S3, day 20, biol rep 2


title: dorsal root ganglia, AEW, rep1

description: 10x Genomics


title: M_4_2_5_6

city: Gainesville

first: Chengguo

last: Xing

state: FL

address: 1345 Center Drive

institute: University of Florida

data_processing:
Sequence reads were mapped to GrCM38/mm10 using HISAT2 for alignment
Picard for count deduplication
HTSeq for extract count
Lowly expressed genes were filtered out using mean of log(cpm+1) < 1
Assembly: mm10
Supplementary files format and content: comma-separated values file includes count values for both lung and liver tissue samples

source_name: liver

growth_protocol: Mice were maintained under standard rodent housing conditions

extract_protocol:
RNA was extracted via standard RNA isolation kit
Novogene standard protocol

treatment_protocol: kava was given via gavage for C57BL mice and in diet for A/J mice

value: A/J mouse

value: liver

tag: diet

value: Kava

tag: smoking

value: Yes

value: 10 – 11 weeks

tag: gender

value: Female

tag: weight


title: 178, S, day 120, biol repl 1, run 1

description: 10x Genomics

source_name: brain organoid tissue

value: day 120

value: striatum protocol (S)


title: Metabolic gene WPS series met4-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:R05G6.5, stt-3, adk-1, T19B4.3, pnp-1, abhd-12, ipla-3, ppat-1, C29F7.3, pus-1, rars-1, MULTIPLE-F54E4.13-F54E4.4, pde-5, upp-1.


title: Metabolic gene WPS series met3-lib6

value: Including empty vector controls and single gene RNAi knockdown for genes:VECTORLIKE-odc-1, spds-1, C31C9.2, Y39B6A.3, mccc-1, phy-2, VECTORLIKE-glna-1, cpin-1, K01C8.1, nsun-5, gst-43, RCBVECTOR-daao-1, pcbd-1, F13H8.9, Y51H4A.7, R102.4.


title: Sensory neurons from H9 hPSCs, day 20, biol rep 4

value: hPSC

value: WT


title: M_4_2_4_6


title: M_4_2_3_6


title: 178, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 16


title: Sensory neurons from FD iPSC S3, day 20, biol rep 1

value: iPSC

value: FD


title: 178, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

value: day 0


title: Sensory neurons from H9 hPSCs, day 20, biol rep 2


title: 178, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: Sensory neurons from FD iPSC S3 treated with genipin, day 20, biol rep 1

value: genipin (10 microM)


title: Metabolic gene WPS series met3-lib5

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:afmd-1, RCBVECTOR-Y51H7C.9, oatr-1, pycr-4, gldc-1, pah-1, T12A2.1, B0228.7, dpy-18, glna-3, ctl-1, F01D4.8, C01G10.9, mett-10, kmo-2.


title: 178, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: Metabolic gene WPS series met3-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:seld-1, F53F10.2, ddo-3, SHORT-parp-2, glna-2, gln-6, riok-1, tph-1, NOSIGNAL-nkat-1, SHORT-F08F3.4, gpx-3, RCBVECTOR-T01D1.4, Y53G8B.1, kmo-1, gst-42, VECTORLIKE-ddo-2.


title: 178, V, day 25, biol repl 1, run 1

description: 10x Genomics

value: day 25

value: ventral protocol (V)


title: Sensory neurons from H9 hPSCs, day 20, biol rep 3

value: hPSC

value: WT


title: M_3_2_2_6

value: A/J mouse

value: liver

value: Kava

value: No

value: 10 – 11 weeks

value: Female


title: M_3_2_1_6


title: Sensory neurons from H9 hPSCs, day 20, biol rep 1


title: Metabolic gene WPS series met3-lib2

value: Including empty vector controls and single gene RNAi knockdown for genes:tdc-1, VECTORLIKE-lbp-1, D2023.4, pycr-1, argn-1, F58H1.3, phy-3, henn-1, ivd-1, smd-1, asns-1, acsd-1, VECTORLIKE-gln-1, VECTORLIKE-tyr-2, ech-5.


title: 178, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 40

value: midbrain protocol (M)


title: M_3_1_2_6


title: Metabolic gene WPS series met3-lib1

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:agxt-1, bas-1, hmgr-1, F42F12.4, C14E2.4, Y62E10A.13, prdh-1, mrpl-44/mccc-2, ZC373.5, nhr-164, nuaf-1, ard-1, K10C2.2, cat-2, VECTORLIKE-iscu-1, alh-6.


title: HEK293T-dox-D7 bulk amplicon-seq

city: Guangzhou

first: Cheng

last: Chen

state: Guangdong

address: Kaiyuan Ave 190

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science

data_processing:
The barcoded processing, gene counting,  and aggregation were made using  the DNBelab_C_Series_HT_scRNA-analysis-software v1.0 (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software) The allele calling of amplicons was made using the Cassiopeia 2.0.0 software (https://github.com/YosefLab/Cassiopeia)
Assembly: mm10/GRCh38
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls (csv).
Library strategy: Amplicon-seq

extract_protocol:
Mouse neuromesodermal organoids were dissociated by Papain dissociation kit (Worthington). In brief, embryoid bodies were incubated in 1 ml Enzyme A along with 20 μl DnaseI at 37℃ for 20-25 min, following by gentle blowing every 5 minutes with wide-bore tips. After washing and filtering, a suitable volume of PBS with 0.04% BSA was added to resuspend the cells to achieve the cell concentration of 2x106 /ml.
Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.

value: cell line

value: human embryonic kidney


title: 178, M, day 16, biol repl 1, run 1

description: 10x Genomics

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

value: day 16


title: HEK293T-dox-D5 bulk amplicon-seq


title: HEK293T-dox-D3 bulk amplicon-seq


title: 178, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: M_2_2_5_6

value: A/J mouse

value: liver

value: Control

value: Yes

value: 10 – 11 weeks


title: 178, D, day 80, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 80


title: Metabolic gene WPS series met2-lib5_redo

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:C56G3.2, NOSIGNAL-acs-3, SHORT-cka-2, acl-2, cpt-2, K07B1.4, C27A7.5, T03G6.3, hphd-1, T12B3.3, F09G2.8, pld-1, SHORT-acl-8, acs-2, unc-17. [Note:this is from the experiment where we redid library construction for part of the samples in met2-lib5, using the original total RNA extraction. These samples correspond to one biological replicate that was missed in met2-lib5 because of a pipetting error.]


title: HEK293T-dox-D1 bulk amplicon-seq

value: cell line

value: D0-D7+4OHT, D8+dox


title: Metabolic gene WPS series met3-lib4

value: Hermaphrodite

value: Including single gene RNAi knockdown for genes:dnj-15, hdl-1, mif-1, W07E11.1, gln-3, Y49E10.4, frh-1, haao-1, hgo-1, tdo-2, tbh-1, B0250.5, bcat-1, amx-2, T25B9.1, pstk-1. [NOTE:This library missed empty vector controls due to a pipetting error.]


title: M_2_2_4_6

value: Female


title: M_4_2_2_6

value: A/J mouse

value: Kava


title: HEK293T-4OHT-D7 bulk amplicon-seq

value: human embryonic kidney


title: 178, D, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40

value: dorsal protocol (D)


title: Metabolic gene WPS series met2-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:C56G3.2, NOSIGNAL-acs-3, SHORT-cka-2, acl-2, cpt-2, K07B1.4, C27A7.5, T03G6.3, hphd-1, T12B3.3, F09G2.8, pld-1, SHORT-acl-8, acs-2, unc-17.


title: Metabolic gene WPS series met2-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:ace-1, K01C8.1, pssy-1, ZK370.4, RCBVECTOR-W02F12.2, C07E3.9, mrpl-55, nlt-1, sptl-1, spl-1, bckd-1A, C17C3.1, dgk-5, mboa-3, C17C3.3, R08F11.1.


title: 178, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 25


title: Metabolic gene WPS series met2-lib3

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:fard-1, RCBVECTOR-eppl-1, ech-3, dgk-2, paf-2, ttm-5, Y45G12B.3, hpo-8, hach-1, acl-9, sms-5, ctb-1, gba-1, R08B4.3, asm-2, C29E4.10.


title: M_2_2_1_6

value: liver

value: Control

value: Yes

value: 10 – 11 weeks


title: HEK293T-4OHT-D5 bulk amplicon-seq

value: cell line


title: HEK293T-4OHT-D3 bulk amplicon-seq

value: human embryonic kidney


title: M_3_1_1_6

value: A/J mouse

value: Kava

value: No

value: Female


title: M_1_2_4_6


title: 177, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: day 120

value: ventral protocol (V)


title: Metabolic gene WPS series met2-lib2

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:pmt-1, hacd-1, nhr-282, ctc-1, ath-1, hyl-2, C31H5.6, acs-15, acl-1, ZC155.4, fat-5, cgt-2, NOSIGNAL-hpo-13, ipla-5, sptl-2, T28F3.5.


title: M_2_2_2_6

value: liver

value: Control

value: Yes


title: Metabolic gene WPS series met2-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:F42F12.3, acl-6, M05B5.4, bckd-1B, NOSIGNAL-T09B4.8, paf-1, R05D11.9, W02H5.8, sms-1, ads-1, sorf-2, alh-7, ctc-2, ceh-48, F55A4.3, lagr-1.


title: HEK293T-4OHT-D1 bulk amplicon-seq

value: cell line

value: human embryonic kidney


title: Metabolic gene WPS series met2-lib6

value: Including empty vector controls and single gene RNAi knockdown for genes:daf-22, ttr-12, fat-1, dgtr-1, hyl-1, acs-5, cept-2, mboa-4, dgk-4, VECTORLIKE-ech-1.1, ipla-4, VECTORLIKE-ech-1.2, ace-2, F10D2.8, T22G5.1.


title: M_1_2_3_6

value: A/J mouse

value: No

value: 10 – 11 weeks

value: Female


title: 178, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 13

value: dorsal protocol (D)


title: 177, V, day 80, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: day 80

value: ventral protocol (V)


title: TSVZ_MIS2B

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description: 10x Genomics

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v7.0.0) (PMID: 28091601). The “mkfastq” command was used to generate FASTQ files and the “count” command was used to generate raw gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters. Mouse genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates (PMID: 33270111).  The data from 3 area (N_SVZ, T_SVZ and T_Mass) were analyzed individually. Samples from patients were combined in R using the Read10X() function from Seurat package(v4.3.0) (PMID: 34062119) and an integrated Seurat object was generated. Filtering was conducted by retaining cells that had unique molecular identifiers (UMIs) less than 25000 and had mitochondrial content less than 5 percent. Doublets were removed using scDblFinder (v1.12.0) (PMID: 35814628). The SCTransform workflow was used for count normalization and data integration (PMID: 31870423) using 30 principal components and resolution of 0.3 for Louvain clustering and UMAP. Batch correction was performed using Harmony (v0.1.1)( PMID: 31740819). Cell cycle analysis was conducted using the CellCycleScoring() with a list of cell cycle markers (PMID: 26430063). Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. N_SVZ is from two patients HNS1 and HNS2 with a total of 19988 genes and 8772 cells. T_SVZ is from 12 patients GBM7B, GBM8B, GBM9B, GBM10B, GBM12B, GBM16B, GBM17B, GBM20B, GBM22B, MIS1B, MIS2B, MIS3B with a total of 19988 genes and 37360 cells. T_Mass is from 14 patients GBM7A, GBM8A, GBM9A, GBM10A, GBM12A, GBM14A, GBM16A, GBM17A, GBM18A, GBM20A, GBM22A, MIS1A, MIS2A, MIS3A with a total of 19988 genes and 67801 cells. For N_SVZ Cell annotation was performed using two different approaches: 1) scType an ultrafast unsupervised method for cell type annotations (PMID: 35273156) 2) Manual curation by gene markers to reflect the prediction results.  Cell type annotation for T_SVZ and T_Mass: Tumor cells were identified using InferCNV analysis (PMID: 31980621) with the following parameters - denoise TRUE, default hidden markov model (HMM) settings, and a value of 0.1 for “cutoff” and the N_SVZ clusters were used are reference. Each resulted CNV was annotated to be either a gain or a loss. Tumor cell clusters were classified based on Neftel GBM cell state (PMID: 31327527) using the their meta module gene markers, SCpubr(V2.0.1) was used to visualize the resultant enrichment. The Clusters that showed an enrichment for that a cell state were labelled as GBMopc(OPClike), GBMac(AClike), GBMmes(MESlike), GBMnpc(NPClike), other clusters that either showed enrichment for two or more cell states or no enrichment for any cell state were labelled as GBMcc(Cancer Cells). Healthy cells were manually curated by using canonical gene markers:. Astrocytes - "GFAP","AQP4", Microglia - "MEF2C","P2RY12", Neurons - "SYNPR","CNR1", "SYT1”, Oligodendrocytes - "MOG","MBP", OPC - "VCAN","SOX5", Endothelial - "VWF","ABCB1", Ependymal  - "SPARCL1","S100B".  All 3 area N_SVZ, T_SVZ and T_Mass were integrated with Harmony (v0.1.1)( PMID: 31740819), 30 PCA and a resolution of 0.3 was chosen.  Genes differentially expressed were calculated between N_SVZ vs T_SVZ, N_SVZ vs T_Mass, and T_SVZ vs T_Mass as a whole area. The R package LIBRA (v1.0.0) was used to perform zero-inflated regression analysis (PMID: 34584091). Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.3.
Assembly: hg38
Supplementary files format and content: Matrix files

molecule: nuclear RNA

source_name: tumor svz sample of glioblastoma patient mis2

extract_protocol:
Nuclei were isolated from frozen human brain tumor and non-tumor tissues. Briefly, frozen human tissue samples were homogenized and lysed with Triton X-100 in RNase-free water for nuclei isolation. The isolated nuclei were purified, centrifuged, and resuspended in PBS with BSA and RNAse Inhibitor. The nuclei were diluted to 700 nuclei/ul and loaded to 10x Genomics Chromium Controller to encapsulate single nuclei into droplet emulsions following the manufacturer’s recommendations.
3’ single nucleus gene expression libraries (Next GEM v3.1, dual index) were constructed using the 10x Genomics Chromium system. Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay and quality assessed by BioAnalyzer.
Each library was sequenced on Illumina NovaSeq 6000 (PE150). Reads were subsequently processed using 10x Genomics Cell Ranger analytical pipeline and human GRCh38 reference genome.

tag: disease

value: glioblastoma


title: 177, V, day 40, biol repl 1, run 1

description: 10x Genomics

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

value: day 40


title: M_1_2_2_6

value: liver

value: Control


title: TSVZ_MIS3B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient mis3


title: Metabolic gene WPS series met1-lib6

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:cgt-3, B0272.3, acdh-12, cdgs-1, sptl-3, acdh-11, dbt-1, gba-4, cka-1, ssq-2, C05C10.3, ace-4, F13H10.5, C37H5.13, MULTIPLE-srd-18-19-20, mmcm-1.


title: Metabolic gene WPS series met1-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:fat-4, acdh-10, kat-1, ech-8, acdh-9, acs-13, cerk-1, atgl-1, agmo-1, elo-9, acs-18, SHORT-mecr-1, elo-8, C03A7.13, strm-1, slx-1.


title: 177, V, day 25, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 25


title: TSVZ_MIS1B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient mis1


title: M_1_2_1_6

value: A/J mouse

value: No

value: 10 – 11 weeks

value: Female


title: Kava+CS-4

source_name: lung

value: lung

value: Kava

value: Yes

value: 10 - 12 weeks

value: Male


title: 177, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: day 13

value: ventral protocol (V)


title: TSVZ_GBM9B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 9

value: glioblastoma


title: Kava+CS-3


title: Metabolic gene WPS series met1-lib3

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:ech-4, elo-5, acdh-6, acl-7, fat-3, T02G5.7, acdh-5, asah-2, F25E2.3, zip-12, T05E7.1, acl-13, elo-4, ckb-2, ckb-1, cgt-1.


title: 177, S, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 120

value: striatum protocol (S)


title: Kava+CS-2

value: lung


title: CS-4

value: Control


title: 177, S, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: TSVZ_GBM7B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 7


title: Metabolic gene WPS series met1-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:asah-1, elo-1, acdh-2, F45H10.2, pcyt-1, acdh-1, gpdh-3, acdh-13, R11F4.1, pccb-1, ckb-3, mce-1, H23N18.4, mlcd-1, nac-2.


title: Metabolic gene WPS series met13-lib6

value: Including empty vector controls and single gene RNAi knockdown for genes:algn-7, kynu-1, elo-6, ivd-1, fum-1, mthf-1, R151.2, pmt-2, pisy-1, ctps-1, B0024.13, sur-5, T24C12.3, F26D11.1, pcs-1.


title: 177, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: day 16


title: TSVZ_GBM22B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 22


title: 177, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

value: female

value: day 0


title: CS-3

value: Yes

value: 10 - 12 weeks

value: Male


title: TSVZ_GBM20B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 20

value: glioblastoma


title: CS-2


title: 177, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: TSVZ_GBM17B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 17


title: Kava-4

value: Kava

value: No


title: Metabolic gene WPS series met13-lib5

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:W02F12.2, mdh-1, T01G1.4, SPECIAL-hxk-1-hxk-2-hxk-3, figo-1, SPECIAL-acly-1-acly-2, W06B4.2, hacd-1, dhs-21, chup-1, suox-1, nnt-1, T09B4.8, coq-3, daao-1, dpyd-1.


title: TSVZ_GBM16B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 16


title: Metabolic gene WPS series met13-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:F52B11.2, elo-1, F57B9.1, dolk-1, aars-1, REALVECTOR-vector, gmps-1, SPECIAL-R05F9.6-Y43F4B.5, MULTIPLE-F02E8.4-F02E8.3, emb-8, let-767, daf-9, tatn-1, mrp-5, Y65B4A.8, nkat-1.


title: Metabolic gene WPS series met1-lib4

value: Including empty vector controls and single gene RNAi knockdown for genes:gta-1, elo-7, F33D4.4, F54D5.7, RCBVECTOR-acdh-7, W03D8.8, ech-9, elo-6, acs-4, gpdh-2, B0303.3, acdh-8, decr-1.3, VECTORLIKE-art-1, B0395.3.


title: Metabolic gene WPS series met13-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:let-268, F59B2.3, metr-1, F08F8.7, F09E5.3, pygl-1, algn-5, mtrr-1, F52C9.3, mcp-1, gst-11, algn-8, REALVECTOR-vector, bcmo-2, R04B3.2, ppk-1.


title: Kava-3

value: lung


title: 177, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: day 80


title: TSVZ_GBM12B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 12


title: TSVZ_GBM8B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 8


title: Metabolic gene WPS series met1-lib2

source_name: Whole animal (excluding eggs)

value: Including empty vector controls and single gene RNAi knockdown for genes:gpdh-1, elo-3, acdh-4, sphk-1, F54D5.12, fat-2, sms-2, lis-1, acdh-3, Y51A2D.13, elo-2, alh-8, psd-1, decr-1.2, nmad-1, F54C8.1.


title: Metabolic gene WPS series met13-lib2

value: Including empty vector controls and single gene RNAi knockdown for genes:Y48B6A.13, mboa-2, trxr-1, bre-4, art-1, Y71G12B.10, algn-11, tpi-1, tag-307, ears-1, C32F10.8, dars-2, aco-1, ech-7, aman-2.


title: Kava-2

value: 10 - 12 weeks

value: Male


title: 177, M, day 16, biol repl 1, run 1

description: 10x Genomics

value: day 16

value: midbrain protocol (M)


title: Kava-1

value: Kava

value: No


title: TMASS_MIS3A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient mis3

value: glioblastoma


title: Metabolic gene WPS series met13-lib1

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:gsy-1, ech-6, pars-2, F26H9.5, gfat-2, bcmo-1, vha-14, Y57G11C.3, coq-5, gfat-1, ipmk-1, mboa-6, cat-1, hmgs-1, folt-1, haly-1.


title: 177, D, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 120

value: dorsal protocol (D)


title: 177, D, day 80, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: day 80


title: TMASS_MIS2A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient mis2


title: NC-3

value: lung

value: Control

value: 10 - 12 weeks


title: Metabolic gene WPS series met11-lib6

value: Including empty vector controls and single gene RNAi knockdown for genes:F26E4.4, nduf-6, rpb-5, elo-3, gale-1, cars-1, rpb-7, acdh-1, ipgm-1, fat-7, wars-1, vha-17, elo-5, elo-3, ugt-62, REALVECTOR-vector.


title: Metabolic gene WPS series met11-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:vha-5, tars-1, pap-1, acdh-1, fntb-1, metr-1, let-611, dif-1, glod-4, crls-1, aak-2, F32D8.12, vars-1, aars-2, REALVECTOR-vector.


title: TMASS_MIS1A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient mis1


title: 177, D, day 40, biol repl 1, run 1

description: 10x Genomics

source_name: brain organoid tissue

value: day 40


title: 177, M, day 40, biol repl 1, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: NC-2

value: No

value: Male


title: 177, D, day 25, biol repl 1, run 1

description: 10x Genomics

value: day 25


title: Metabolic gene WPS series met11-lib4

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:glp-4, pod-2, asp-1, mtrr-1, cept-1, rpb-8, ugt-12, dld-1, gcst-1, upb-1, fah-1, fars-3, rpc-1, vha-5, vha-19, rpc-25.


title: ESC-dox-D8 bulk amplicon-seq

source_name: cell line

value: cell line

value: mouse embryonic stem cell


title: TMASS_GBM8A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 8

value: glioblastoma


title: 176, V, day 120, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 120

value: ventral protocol (V)


title: TMASS_GBM9A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 9


title: Metabolic gene WPS series met11-lib3

value: Including empty vector controls and single gene RNAi knockdown for genes:mak-1, fat-6, ant-1.1, ugt-46, cpt-2, let-363, ugt-22, adk-1, mccc-1, Y82E9BR.3, ept-1, dlat-1, vha-2, REALVECTOR-vector [technical replicates], C05C8.7.


title: ESC-dox-D6 bulk amplicon-seq


title: TSVZ_GBM10B

description: 10x Genomics

source_name: tumor svz sample of glioblastoma patient 10


title: Metabolic gene WPS series met11-lib2

value: Including empty vector controls and single gene RNAi knockdown for genes:mpk-1, eat-6, pri-2, ugt-47, fat-3, ggtb-1, sbp-1, gld-2, fars-1, T25B9.9, pdha-1, lpin-1, mmcm-1, REALVECTOR-vector [technical replicates].


title: TMASS_GBM7A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 7


title: ESC-dox-D2 bulk amplicon-seq


title: TMASS_GBM20A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 20


title: ESC-dox-D4 bulk amplicon-seq


title: TMASS_GBM22A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 22


title: NC-4

source_name: lung

value: lung

value: Control

value: No

value: 10 - 12 weeks


title: Metabolic gene WPS series met11-lib1

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:REALVECTOR-vector [technical replicates], rpoa-2, bli-3, ugt-17, elo-5, mdh-2, yars-2, ugt-50, F38B6.4, elo-7, dars-1, nkb-1, atp-1, tag-335, pdhb-1.


title: Metabolic gene WPS series met10-lib6

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:gna-1, hex-3, sars-2, mans-1, C14B9.2, secs-1, dhs-19, iars-2, cah-6, algn-1, chil-23, chil-25, lmd-5, unc-4, chil-21, Y106G6E.4.


title: 176, V, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: 176, V, day 40, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 40


title: Metabolic gene WPS series met10-lib5

value: Including empty vector controls and single gene RNAi knockdown for genes:gna-2, SHORT-dars-2, chil-11, MULTIPLE-chil-19-21, chil-12, C13B9.2, C56A3.8, T05H4.7, F53F1.3, vps-34, gpap-1, fmo-2, chil-16, chil-18, SHORT-chil-5, mtm-6.


title: 176, V, day 25, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 25


title: ESC-4OHT-D8 bulk amplicon-seq

value: cell line

value: mouse embryonic stem cell


title: ESC-4OHT-D6 bulk amplicon-seq


title: 177, D, day 13, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: day 13

value: dorsal protocol (D)


title: 176, V, day 13, biol repl 1, run 1

description: 10x Genomics

value: ventral protocol (V)


title: TMASS_GBM17A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 17

value: glioblastoma


title: Metabolic gene WPS series met10-lib3

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Including empty vector controls and single gene RNAi knockdown for genes:gly-14, T03F6.3, pigl-1, C08F8.2, K09A9.6, C10C5.3, alh-13, chil-22, mans-3, F53C11.3, SHORT-clec-123, ZC443.1, hex-2, ZC8.6, Y48G10A.1, chs-2.


title: TMASS_GBM16A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 16


title: ESC-4OHT-D4 bulk amplicon-seq


title: 176, S, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80

value: striatum protocol (S)


title: Metabolic gene WPS series met10-lib2

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:chil-8, sqv-4, SHORT-heri-1, F39F10.4, mans-4, gbh-1, Y49E10.4, tyr-4, F21D5.1, F39B2.3, cht-1, aagr-4, moc-2, chil-2, cpt-5.


title: nmoD15c amplicon-seq

description: DNBelab C4

data_processing:
The barcoded processing, gene counting,  and aggregation were made using  the DNBelab_C_Series_HT_scRNA-analysis-software v1.0 (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software) The allele calling of amplicons was made using the Cassiopeia 2.0.0 software (https://github.com/YosefLab/Cassiopeia)
Assembly: mm10/GRCh38
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls (csv).

source_name: in vitro organoid

value: in vitro organoid

value: organoid

value: nmpD0-D3+4-OHT, nmoD2-D8 +Dox


title: ESC-4OHT-D2 bulk amplicon-seq

value: cell line


title: Metabolic gene WPS series met10-lib1

value: Including empty vector controls and single gene RNAi knockdown for genes:chil-27, gly-20, ephx-1, gly-13, dpm-1, dhrs-4, fmo-4, sqv-1, mogs-1, algn-13, VECTORLIKE-cht-4, C44E12.1, parg-1, ipp-5, dpm-3.


title: TMASS_GBM12A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 12


title: 176, S, day 16, biol repl 1, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 16


title: nmoD15b amplicon-seq

description: DNBelab C4


title: 176, S, day 40, biol repl 1, run 1

description: 10x Genomics

value: day 40


title: Hfx. mediterranei cells, rosR deletion strain, whole cell extract control, rep4

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

data_processing:
50 bp reads were assessed for quality using FastQC and adapter sequences trimmed using Trim Galore and Cutadapt. Resultant reads were mapped to the Hfx. mediterranei ATCC3500 (assembly ASM30676v2; NCBI accession GCF_000306765.2) or Hfx. volcanii DS2 genome (ASM2568v1; GCF_000025685.1) using Bowtie2.
Sorting of mapped sequences was conducted using samtools. Sites of significant RosR binding enrichment were called using the MOSAiCS peak-calling package [REF] with sorted bam files as input. MOSAiCS parameters included fragment length (fragLen) 200, cap 0, PET false, analysis type IO, background estimate rMOM, FDR 0.01.
Using the DiffBind R package, peaks were considered reproducible if 100 bp of the reads in the peak overlapped across three of four biological replicate experiments. Using the GenomicRanges and IRanges R packages, a given peak was associated with a given genomic feature (gene or promoter region) if the they overlapped by 100 bp. Peaks that fell entirely inside promoter regions were associated with the nearest gene within 500 bp.
Peak-to-gene associations were then annotated using the corresponding NCBI genome annotation within the GenomicFeatures R package.
Assembly: Hfx. mediterranei ATCC3500 (assembly ASM30676v2; NCBI accession GCF_000306765.2); Hfx. volcanii DS2 genome (ASM2568v1; GCF_000025685.1)
Supplementary files format and content: sorted bam files

organism: Haloferax mediterranei ATCC 33500

source_name: archaeal cells

growth_protocol: Each Hfx. strain (parental ΔpyrE and RosR::HA tagged) was grown in quadruplicate (ChIP-seq) in 50 mL rich medium until mid- to late-exponential phase (OD600 ~0.5-1.0).

extract_protocol:
chromatin immunoprecipitation (ChIP) and DNA extraction was conducted as previously described (Martinez Pastor M. et al., 2017).
For ChIP-seq, Libraries were constructed using the KAPA Hyper Prep kit using Illumina TruSeq adapters. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent).
Samples for each species were multiplexed according to the adapter mixtures and pooled. Each pool was run on a single lane on an Illumina HiSeq 4000 instrument by the Duke Sequencing and Genomics Techonology core facility

treatment_protocol: Crosslinking was performed by adding 37% formaldehyde (CH2O) for 20 min at room temperature.

value: archaeal cells

value: {delta}pyrE HMErosR::HA

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: Nsvz_HNS2

description: 10x Genomics

source_name: histologically normal human brain sample

value: normal


title: nmoD15a amplicon-seq

description: DNBelab C4


title: TMASS_GBM18A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 18

value: glioblastoma


title: Hfx. mediterranei cells, rosR deletion strain, immunoprecipitation, rep4


title: Metabolic gene WPS series met10-lib4

source_name: Whole animal (excluding eggs)

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for genes:algn-14, ceeh-1, lars-2, C36A4.4, plc-3, C10C5.4, algn-3, lin-46, mans-2, acs-20, chil-13, ears-2, SHORT-hex-5, SHORT-hex-5, strm-1, chil-6.


title: TMASS_GBM10A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 10


title: Hfx. mediterranei cells, rosR deletion strain, immunoprecipitation, rep3


title: nmpD3 amplicon-seq

description: DNBelab C4

value: in vitro organoid

value: organoid


title: Nsvz_HNS1

description: 10x Genomics

value: histologically normal human brain sample


title: 176, pluripotent, day 0, biol repl 1, run 1

description: 10x Genomics

source_name: brain organoid tissue

value: brain organoid tissue

value: day 0


title: 176, M, day 120, biol repl 1, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: day 120

value: midbrain protocol (M)


title: Sf3b4 homozygous null embryo (rep 3)

city: Montreal

first: Loydie

last: Jerome-Majewska

state: QC

address: 1001 Decarie Blvd EM0.2210

department: Pediatrics

country: Canada

institute: McGill University Health Centre Glen Site

data_processing:
bcbio nextgen 1.2.9
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: embryo head

extract_protocol:
RNA was extracted using RNAesay micro kit (Qiagen) according to manufacturer's protocol
libraries were constructed using TruSeq Standard Total RNA sample preparation kit (Illumina) according to manufacturer's protocol

value: embryo head

value: Sf3b4 NCC mutant


title: Hfx. mediterranei cells, rosR deletion strain, whole cell extract control, rep3

value: archaeal cells

value: {delta}pyrE HMErosR::HA

value: standard growth medium, mid-exponential phase, RosR eptiope tagged with HA


title: 176, M, day 80, biol repl 1, run 1

description: 10x Genomics

value: day 80


title: Sf3b4 homozygous null embryo (rep 2)


title: TMASS_GBM14A

description: 10x Genomics

source_name: tumor mass sample of glioblastoma patient 14

value: glioblastoma