title: WT H-NS Rep 3

description: HNS ChIP in WT CFT073 rep 3


title: C646 + 4hr WO Rep 1

status: Public on Oct 06 2022

type: SRA

city: Stockholm

first: Mattias

last: Mannervik

address: Svante Arrhenius väg 20C

department: Dept. of Molecular Biosciences

country: Sweden

institute: Stockholm University

description: C646 + 4hr WO Rep 1

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped to the Drosophila dm6 genome assembly using the STAR RNA-seq aligner with the default parameters. Coverage tracks of the mean RPKM signal from the three biological replicates were produced using deepTools. Reads mapping to the exons of genes were counted using featureCounts and differential gene expression analysis performed on the count data using the DESeq2 Bioconductor package.
Assembly: dm6
Supplementary files format and content: bigwig for coverage

molecule: total RNA

organism: Drosophila melanogaster

source_name: Schneider 2 (S2) cells

growth_protocol: S2 cells were cultured at 25°C in Schneider's Drosophila medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Total RNA corresponding to 0.5-1 million control or drug treated S2 cells were homogenized in TRIzol LS (Ambion) and purified and concentrated using the RNeasy MinElute Cleanup kit (Qiagen) according to the manufacturer's instructions. RNA extractions were performed on three independent biological replicates.
RNA libraries were prepared from total RNA using the Illumina Stranded mRNA Prep kit and sequenced single-end (1 x 75 bp) on the Illumina NextSeq 2000 platform.

treatment_protocol: Experiments were conducted on cells at 80-90% confluency. Cells were resuspended in FBS-free media and incubated with 30 μM of C646 for 30 minutes, with or without a drug washout (WO) in media without C646 for either 1 hr or 4 hr.

tag: strain

value: Oregon R

tag: developmental stage

value: Late embryonic stage


title: C646 + 1hr WO Rep 2

description: C646 + 1hr WO Rep 2


title: C646 + 1hr WO Rep 1

description: C646 + 1hr WO Rep 1


title: C646 30 min Rep 3

description: C646 30 min Rep 3


title: C646 30 min Rep 1

description: C646 30 min Rep 1


title: Control Rep 3

description: Control Rep 3


title: C646 30 min Rep 2

description: C646 30 min Rep 2


title: Control Rep 2

description: Control Rep 2


title: C646 + 1hr WO Rep 3

description: C646 + 1hr WO Rep 3


title: Control Rep 1

description: Control Rep 1


title: Blood_LOW_MeHg_9

type: genomic

city: Portland

first: Caren

last: Weinhouse

state: OR

address: 3181 SW Sam Jackson Park Road L606

country: USA

institute: Oregon Health & Science University

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R04C01

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Standard pipeline in R package RnBeads. Processed data are reported for both differential and differentially variable CpG sites and genomic regions (tiling, genes, promoters, CpG islands).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood from study participant with low (<1 ppm) total hair mercury

label_protocol: Standard Illumina protocol

extract_protocol: whole blood collected in BD Trace Element Vacutainer tubes, frozen at -20°C within 6 hours of collection. DNA extracted with Qiagen DNEasy kits and bisulfite converted using Zymo EZ DNA methylation kits.

tag: Sex

value: M

tag: age

tag: continuous total hair mercury


title: Blood_LOW_MeHg_16

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R08C01

value: F


title: Blood_LOW_MeHg_4

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R05C01


title: Blood_LOW_MeHg_10

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R03C01


title: Blood_LOW_MeHg_13

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R01C01


title: Blood_HIGH_MeHg_12

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R07C01

source_name: Whole blood from study participant with high (>10 ppm) total hair mercury


title: Blood_HIGH_MeHg_13

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R04C01


title: Blood_LOW_MeHg_7

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R08C01


title: Blood_LOW_MeHg_2

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R02C01


title: Blood_LOW_MeHg_11

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R06C01


title: Blood_LOW_MeHg_12

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R04C01


title: Blood_HIGH_MeHg_15

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R07C01


title: TSC2_HighPolysome-196463

city: Vienna

first: Jaydeep

last: Sidhaye

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
Smart-seq3 read analysis was performed using zUMI v2.9.7  (https://github.com/sdparekh/zUMIs), providing the expected barcodes file, using STAR 2.7.7a with additional STAR parameters "--limitOutSJcollapsed 50000000 --limitIObufferSize 1500000000 --limitSjdbInsertNsj 2000000 --clip3pAdapterSeq CTGTCTCTTATACACATCT''
Assembly: GRCh38
Supplementary files format and content: zUMI.UMIc.inex.tsv

source_name: Day30 brain organoids

extract_protocol:
Phenol chloroform precipitation
SMARTseq3-V3

treatment_protocol: Monosome, low-polysome and high polysome fractions were separated using sucrose gradient fractionation

tag: tissue

value: Day30 brain organoids

tag: cell line

value: Rozh5 iPSC

tag: cell type

value: Brain organoids

tag: genotype

value: TSC2 KO

tag: fraction

value: high-polysome fraction from polysome profiling


title: TSC2_LowPolysome-196462

value: low-polysome fraction from polysome profiling


title: Blood_HIGH_MeHg_4

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R02C01


title: Blood_LOW_MeHg_1

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R06C01


title: Blood_LOW_MeHg_6

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R08C01


title: TSC2_Monosome-196461

value: Monosome fraction from polysome profiling


title: WT_HighPolysome-196459

value: WT


title: Blood_LOW_MeHg_14

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R03C01


title: Blood_LOW_MeHg_3

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R07C01


title: Blood_HIGH_MeHg_10

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R02C01


title: Blood_HIGH_MeHg_14

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R01C01


title: Blood_LOW_MeHg_8

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R01C01


title: Blood_HIGH_MeHg_5

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340028_R03C01


title: WT_Monosome-196457


title: TSC2_HighPolysome-196455


title: Blood_LOW_MeHg_5

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R06C01


title: WT_LowPolysome-196458


title: Blood_LOW_MeHg_15

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R06C01


title: TSC2_LowPolysome-196454


title: TSC2_Monosome-196453


title: WT_LowPolysome-196450


title: WT_Monosome-196449


title: WT_HighPolysome-196451


title: Blood_HIGH_MeHg_16

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R08C01


title: TSC2_HighPolysome-196447


title: Blood_HIGH_MeHg_3

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R04C01


title: Blood_HIGH_MeHg_11

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R03C01


title: WT_LowPolysome-196442


title: THP-1 cells, RNAseq/LPSDex, 3h, rep3

city: Neuherberg

first: Suhail

middle: A.

last: Ansari

address: Ingolstaedter Landstr.1

department: Institute for Diabetes and Endocrinology (IDE)

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Ribo-seq reads were clipped to remove residual adapters using the FASTX toolkit.
The paired mRNA-seq reads (2x101nt) were trimmed to 29-mers (the average length of Ribo-seq reads) in order to reduce any read length or filtering bias towards mapping or quantification. This was done in order to establish the comparability of the data obtained from Ribo-seq and RNA-seq.
Trimmed RNA-seq reads were then mapped to the human reference genome (GRCh38, Ensembl v87) using STAR v2.7.10a.
The quantification of gene expression was accomplished by using featureCounts v2.0.1. DESeq2 v1.26.0 was used to normalize gene counts with respect to size factor or other normalization parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited text file of raw count matrix.

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium (Thermo Fisher Scientific) supplemented with 10% heat inactivated FBS (Sigma Aldrich), 1% Pen/Strep (Sigma Aldrich). The cells were grown at 37 C and 5% CO2 and routinely tested negative for mycoplasma contamination.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen) using 3M of the exact same human THP-1 cells processed for ribosome profiling. RIN scores were measured on a BioAnalyzer 2100 using the RNA 6000 Nano assay (Agilent). Poly(A)-purified mRNA-seq libraries were generated from high quality RNA (average RNA Integrity Number (RIN)) of 7.7.
RNA-seq library preparation was performed according to the TruSeq Stranded mRNA Reference Guide, using 500ng of total RNA as input.
Libraries were multiplexed and sequenced on an Illumina NovaSeq 6000 producing paired 2x101nt reads. THP-1 mRNA-seq libraries were sequenced to an average depth of 160M (min. 81M, max. 207M) raw reads.
RNA-seq library was prepared according to the protocol as described in TruSeq Stranded mRNA Reference Guide.

treatment_protocol:
For THP-1 differentiation, cells were grown in culture media containing the dialyzed FBS (Sigma Aldrich) and incubated with 10 ng/ml (final concentration) phorbol 12-myristate 13-acetate (PMA, Sigma Aldrich) for 24h, followed by incubation with fresh growth media (without PMA).
The differentiated THP-1 cells were treated with vehicle control (0.1% ethanol/PBS), 100 ng/ml lipopolysaccharide (LPS, Sigma Aldrich) and 1 µM Dex (Sigma Aldrich) and incubated for 3h.

value: Human leukemia monocytic cell line

tag: treatment

value: LPS+Dex

tag: time


title: Blood_HIGH_MeHg_6

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R02C01


title: THP-1 cells, RNAseq/LPSDex, 3h, rep4


title: THP-1 cells, RNAseq/LPSDex, 3h, rep1


title: THP-1 cells, RNAseq/LPS, 3h, rep4

value: LPS


title: TSC2_Monosome-196445


title: THP-1 cells, RNAseq/LPS, 3h, rep3


title: WT_HighPolysome-196443


title: Blood_HIGH_MeHg_8

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R01C01


title: TSC2_LowPolysome-196446


title: Blood_HIGH_MeHg_7

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340031_R05C01


title: THP-1 cells, RNAseq/LPS, 3h, rep2


title: THP-1 cells, RNAseq/Vehicle, 3h, rep2

value: Vehicle


title: THP-1 cells, RNAseq/LPSDex, 3h, rep2


title: THP-1 cells, RNAseq/Vehicle, 3h, rep3


title: Blood_HIGH_MeHg_9

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R07C01


title: THP-1 cells, RNAseq/Vehicle, 3h, rep1


title: THP-1 cells, RNAseq/LPS, 3h, rep1


title: THP-1 cells, Riboseq/LPSDex, 3h, rep4

data_processing:
Ribo-seq reads were clipped to remove residual adapters using the FASTX toolkit. Reads mapping to the ribosomal RNA (rRNA) and tRNA sequences were removed with Bowtie2 v2.4.5.
Trimmed  Ribo-seq reads were then mapped to the human reference genome (GRCh38, Ensembl v87) using STAR v2.7.10a.
The quantification of gene expression was accomplished by using featureCounts v2.0.1.
DESeq2 v1.26.0 was used to normalize gene counts with respect to size factor or other normalization parameters for Ribo-seq data.
hg38
tab-delimited text file of raw count matrix.

extract_protocol:
The lysate was homogenized by immediate repeated pipetting and multiple passes through a syringe fitted with a 21G needle, allowing for dissociation of cell clumps and facilitating quick and equal lysis of the cells. Samples were next centrifuged at 20,000g for 10 minutes at 4°C to pellet cell debris.
Per sample, 200 or 400µL of lysate were digested with RNase 1 (Biozym), purified with Microspin Sephacryl S-400 HR columns (Sigma-Aldrich) and 1µg footprints were used for removal of the ribosomal RNA according to the Ribo-Zero Gold rRNA Removal Kit (h/m/r) (Illumina).
The footprints were purified by excision from a Novex 15% TBE Urea PAGE gel (Fisher Scientific) followed by a treatment of the 3´ends with T4 PNK (Biozym) to allow ligation to a pre-adenylated linker.
The RNA was then reverse transcripted with RNase H Reverse Transcriptase (Biozym)  and the cDNA purified via a Novex 10% TBE Urea PAGE gel (Fisher Scientific). The fragments were circularized using Circligase I (Biozym) followed by a PCR amplification and size selection using a Novex 8% TBE PAGE gel (Fisher Scientific).
For all samples, ribosome profiling library size distributions were checked on the Bioanalyzer 2100 using a high sensitivity DNA assay (Agilent), multiplexed and sequenced on a NovaSeq 6000 producing single end 1x51nt reads. Ribo-seq libraries were sequenced to an average depth of 80M (min. 64M, max. 91M) raw reads.
Ribosome profiling library was constructed according to previously described work (McGlincy NJ, 2017; van Heesch S, 2019; Gaertner B, 2020 ). See also the extraction protocol.

treatment_protocol:
The differentiated THP-1 cells were treated with vehicle control (0.1% ethanol/PBS), 100 ng/ml lipopolysaccharide (LPS, Sigma Aldrich) and 1 µM Dex (Sigma Aldrich) and incubated for 3h.
10M cells were lysed for 10 minutes on ice in 1 mL lysis buffer consisting of 20mM Tris-Cl (pH 7.4), 150mM NaCl, 5mM MgCl2, 1% Triton X-100, 0.1% NP-40, 1mM dithiothreitol, 10U/ml DNase I, cycloheximide (0.1mg/ml) and nuclease-free H2O.


title: THP-1 cells, Riboseq/LPSDex, 3h, rep5


title: THP-1 cells, RNAseq/Vehicle, 3h, rep4


title: THP-1 cells, Riboseq/LPSDex, 3h, rep3


title: THP-1 cells, Riboseq/LPSDex, 3h, rep2


title: THP-1 cells, Riboseq/LPSDex, 3h, rep1


title: THP-1 cells, Riboseq/LPS, 3h, rep5


title: THP-1 cells, Riboseq/LPS, 3h, rep2


title: THP-1 cells, Riboseq/Vehicle, 3h, rep1

growth_protocol: For THP-1 differentiation, cells were grown in culture media containing the dialyzed FBS (Sigma Aldrich) and incubated with 10 ng/ml (final concentration) phorbol 12-myristate 13-acetate (PMA, Sigma Aldrich) for 24h, followed by incubation with fresh RPMI media.


title: THP-1 cells, Riboseq/LPS, 3h, rep3


title: THP-1 cells, Riboseq/Vehicle, 3h, rep5


title: THP-1 cells, Riboseq/Vehicle, 3h, rep3


title: THP-1 cells, Riboseq/LPS, 3h, rep1


title: GM_pH74_24h_Tr4

city: THUWAL

first: Samhan

middle: M.

last: Alsolami

address: Thuwal 23955

department: BESE

country: Saudi Arabia

institute: KAUST

data_processing:
DATA was processed in A.I.R, a platform provided by sequentia
Assembly: hg19
Supplementary files format and content: TMM and FPKM normalized data

source_name: EBV transformed B cell line

growth_protocol: GM12878 cells were grown for 44 hours in batch culture and then cultured for 72 hours in bioreactor exposed to varied treatment of pH

extract_protocol:
GM12878 RNA was extracted using qiagen kit.
paired end stranded library was constructed

treatment_protocol: GM12878 cells were cultured in RPMI 10% FBS.

tag: ph

value: EBV transformed B cell


title: Blood_HIGH_MeHg_2

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340050_R05C01


title: GM_pH7_24h_Tr4


title: GM_0h_Tr4


title: GM_pH74_72h_Tr4


title: THP-1 cells, Riboseq/Vehicle, 3h, rep2


title: GM_0h_Tr1


title: GM_pH72_48h_Tr4


title: THP-1 cells, Riboseq/Vehicle, 3h, rep4


title: GM_pH68_48h_Tr3


title: GM_0h_Tr2


title: GM_pH74_48h_Tr4


title: GM_pH68_48h_Tr2


title: GM_pH7_24h_Tr2


title: GM_pH74_48h_Tr2


title: GM_pH7_48h_Tr1


title: GM_pH7_24h_Tr1


title: THP-1 cells, Riboseq/LPS, 3h, rep4


title: GM_pH68_48h_Tr4


title: Blood_HIGH_MeHg_1

description:
Whole blood from study participant living in the southern Peruvian Amazon near artisanal and small scale gold mining operations
201516340014_R05C01


title: GM_pH68_24h_Tr2


title: GM_pH72_72h_Tr2


title: GM_pH72_48h_Tr3


title: GM_pH72_48h_Tr1


title: GM_pH74_48h_Tr1


title: GM_pH72_72h_Tr4


title: Mt_miRR-NSP2ox_+P+N_2_rep2

city: Cambridge

first: Darius

last: Zarrabian

address: 93 Lawrence Weaver Rd

department: Plant Sciences

country: United Kingdom

institute: Crop Science Centre, University of Cambridge

data_processing:
Quality control was conducted with FastQC software
Resultant raw fastq data were mapped to the M. truncatula reference genome version 4.0 or the H. vulgare cv. Golden Promise reference genome with STAR software
The raw count values were calculated with featureCounts in R package Rsubread
Assembly: Mt4.0v1, Hordeum vulgare cv. Golden  Promise
Supplementary files format and content: tab separated files with raw count values

organism: Medicago truncatula

source_name: hairy root

extract_protocol:
H. vulgare total RNA was extracted using the Spectrum™ Plant Total RNA kit (SigmaAldrich) and M. truncatula total RNA was isolated with the RNeasy PlantMini Kit (Qiagen),  following the manufacturer’s instructions.
Poly A enrichment

value: hairy root

value: A17 ecotype transformed with pBdEF1a:3xMyc-MtNSP2-miRR

value: +P+N

value: 21 days


title: GM_pH7_72h_Tr4


title: Mt_NSP2ox_+P+N_2_rep3

value: A17 ecotype transformed with pBdEF1a:3xMyc-MtNSP2


title: GM_pH74_24h_Tr1


title: Mt_NSP2ox_+P+N_2_rep1


title: Mt_NSP1ox_+P+N_2_rep3

value: A17 ecotype transformed with pLjUBI:3xFLAG-MtNSP1


title: GM_pH72_72h_Tr1


title: GM_pH68_72h_Tr2


title: GM_pH68_24h_Tr3


title: GM_pH74_24h_Tr3


title: Mt_NSP1ox_+P+N_2_rep2


title: GM_pH68_72h_Tr3


title: Mt_NSP1ox_+P+N_2_rep1


title: GM_pH72_72h_Tr3


title: Mt_NSP2ox_+P+N_2_rep2


title: GM_pH7_72h_Tr1


title: Mt_A17_+P+N_2_rep3

value: A17 ecotype transformed with empty vector


title: GM_0h_Tr3


title: Mt_A17_+P+N_2_rep1


title: GM_pH68_72h_Tr4


title: Mt_miRR-NSP2ox_+P+N_2_rep3


title: GM_pH7_24h_Tr3


title: Mt_nsp2_-P-N_rep3

source_name: whole root

value: whole root

value: nsp2-2 mutant in A17 background

value: -P-N

value: 15 days


title: Mt_miRR-NSP2ox_+P+N_2_rep1


title: GM_pH72_24h_Tr3


title: GM_pH7_48h_Tr4


title: GM_pH68_24h_Tr1


title: GM_pH68_24h_Tr4


title: Mt_nsp2_-P+N_rep3

value: -P+N


title: Mt_nsp2_-P-N_rep1


title: GM_pH74_72h_Tr3


title: GM_pH68_48h_Tr1


title: Mt_nsp2_-P+N_rep1


title: GM_pH7_48h_Tr3


title: Mt_nsp2_+P-N_rep1

value: +P-N


title: Mt_nsp2_+P-N_rep2


title: GM_pH72_24h_Tr1


title: GM_pH72_24h_Tr4


title: Mt_nsp2_+P-N_rep3


title: Mt_A17_+P+N_2_rep2


title: Mt_nsp2_+P+N_rep3


title: GM_pH74_48h_Tr3


title: Mt_nsp2_+P+N_rep2


title: Mt_nsp2_+P+N_rep1


title: GRAMD1B_KO2

city: New York

first: Shruthy

last: Suresh

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: processed data files have normalized counts and Differentially expressed gene table matrices from DESEQ2

data_processing:
RNA-sequencing reads in fastq format were trimmed
Trimmed reads quantified by Salmon to a pre-built index of the hg38 human transcriptome from Ensembl accounting for GC biases
Resulting count matrices were used as input for DESEQ2
Assembly: hg38
Supplementary files format and content: norm_counts_GRAMD1B.txt: tab delimited file (table matrix) with normalized counts from DESEQ2 of all samples
Supplementary files format and content: DE_GRAMD1B_KO_NT_0.05.txt : tab delimited file (table matrix) results of differential expression analysis of GRAMD1B KO vs NT in DESEQ2 with padj cutoff 0.05

growth_protocol: cells were grown in complete DMEM with 10% FBS and 1% Pen/Strep.

extract_protocol:
Cells were harvested and RNA isolation was performed using Zymo kit, 1ug RNA per sample was submitted
RNA libraries for RNA-seq were prepared according to Novaseq6000 procedure

treatment_protocol: Cells were infected with LentiCRISPR V2 NT sgRNA or GRAMD1B sgRNA and selected in Puromycin for 10 days prior to harvesting

value: melanoma cell

value: NRAS Q61R, p53, TERT

tag: group

value: sgRNA against GRAMD1B


title: GRAMD1B_KO1


title: GRAMD1B_KO3


title: Mt_nsp1_-P-N_rep2

value: nsp1-1 mutant in A17 background


title: Mt_nsp2_-P-N_rep2


title: Mt_nsp1_-P-N_rep3


title: NT3

value: NT sgRNA


title: NT2


title: WT_Monosome-196441

value: Day30 brain organoids

value: Rozh5 iPSC

value: Brain organoids

value: WT

value: Monosome fraction from polysome profiling


title: Mt_nsp2_-P+N_rep2


title: Mt_nsp1_-P-N_rep1


title: NT1


title: Mt_nsp1_-P+N_rep2


title: Exp7 PB on NONE (LTR31.LC31) rep 3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description:
AAV_AAVS1.tsv
Exp7_LTR31LC31_UThuman_NONE_PB

library_source: genomic

data_processing:
Library strategy: SLiM-PCR, custom amplicon sequencing
FASTQ files processed by RAAVIoli software
Custom software for matrix creation
Genome_build: Hg19 + custom reference AAV genome or IDLV genome
Supplementary_files_format_and_content: Data matrix if integrations (rows) observed in specific samples (columns) and quantified by the number of cells (values).

source_name: Untransduced

extract_protocol:
gDNA was sheared using a Covaris E220 Ultrasonicator (Covaris Inc.), generating fragments with a target size of 1,000 bp.
The fragmented DNA was subjected to end repair, 3’ adenylation and ligation (NEBNext® Ultra™ DNA Library Prep Kit for Illumina, New England Biolabs) to custom linker cassettes (LC) (Integrated DNA Technologies). LC sequences containing 8-nucleotide barcode for sample identification. Ligation products were subjected to 35 cycles of exponential PCR with primers complementary to different regions of the AAV or IDLV genomes and to the LC. For each set of AAV or IDLV specific primers, the procedure was performed in technical replicates (n = 2-3) using 80-100 ng of sheared DNA/each. Next, ten additional PCR cycles were done to include sequences required for sequencing and a second 8-nucleotide DNA barcode. PCR products were quantified by qPCR using the Kapa Biosystems Library Quantification Kit for Illumina, following the manufacturer’s instructions. qPCR was performed in triplicate on each PCR product diluted 10:3, and the concentrations were calculated by plotting the average Ct values against the provided standard curve. The amplification products were sequenced by Illumina Next/Novaseq platforms (Illumina).

value: PB

tag: vector

tag: vector id

tag: subject


title: Mt_nsp1_-P+N_rep1

value: whole root


title: Mt_nsp1_-P+N_rep3


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC27) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR23LC27_ID29_2738.AAV.PGK.GFP_Spleen

source_name: AAV PGK GFP

value: Spleen

value: AAV


title: Exp7 Spleen on NONE (LTR17.LC29) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR17LC29_ID31_NONE_Spleen


title: Mt_nsp1_+P-N_rep3

value: 15 days


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC26) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR53LC26_ID28_2738.AAV.PGK.GFP_Spleen


title: Mt_nsp1_+P-N_rep2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC24) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR41LC24_ID26_2738.AAV.PGK.GFP_Spleen


title: Mt_nsp1_+P-N_rep1


title: Mt_nsp1_+P+N_rep3

value: +P+N


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC23) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR17LC23_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC25) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR31LC25_ID27_2738.AAV.PGK.GFP_Spleen


title: Mt_nsp1_+P+N_rep1


title: Mt_nsp1_+P+N_rep2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC21) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR23LC21_ID7_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_-P-N_rep2

value: wildtype A17 ecotype

value: -P-N


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC20) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR53LC20_ID6_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_-P-N_rep3


title: Mt_A17_-P-N_rep1


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC18) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR41LC18_ID23_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC19) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR31LC19_ID24_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_-P+N_rep3

value: -P+N


title: Mt_A17_-P+N_rep2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC17) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR17LC17_ID21_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_-P+N_rep1


title: Mt_A17_+P-N_rep2

value: +P-N


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR91.LC16) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR91LC16_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC14) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR53LC14_ID2_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC15) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR23LC15_ID3_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_+P-N_rep1


title: Exp7 PB on NONE (LTR41.LC12) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR41LC12_UThuman_NONE_PB


title: Mt_A17_+P+N_rep3


title: Exp7 Spleen on NONE (LTR91.LC10) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR91LC10_ID31_NONE_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR91.LC22) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR91LC22_ID9_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC8) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR53LC8_ID29_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_+P+N_rep1


title: Adam17 ex/ex pancreas, Cerulein, replicate 4

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was performed with Dragen BCLConvert (v3.7.4).
RNA-seq read alignment and UMI counting was performed in R (v4.1.2). The scPipe package (v1.16.0) was employed to process the data. Multiplex RNA-seq FASTQ files had already been demultiplexed and contained the I1 index and UMI sequences in the read header, but headers were reformatted using awk for compatibility with scPipe.
Read alignment was performed using the RSubread package (v2.8.1). An index was built using the Ensembl Mus musculus GRCm38 primary assembly genome file and alignment was performed with default settings.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm38 v100 GFF3 genome annotation file. BAM files were processed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
UMI gene counts were processed in R using the edgeR package (v3.36.0). Additional gene annotation was obtained using the biomaRt package (v2.50.1). Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method.
Differential gene expression analyses were performed using the edgeR voomLmFit function and the limma package (v3.50.0), with the contrasts.fit, eBayes and treat functions.
Assembly: mm10
Supplementary files format and content: Matrix table with UMI gene counts for every gene and every sample.

organism: Mus musculus

source_name: pancreas

growth_protocol: Age-matched (6-8 weeks old) littermates of C57BL/6J wild-type (WT) and Adam17ex/ex mice, which harbor the hypomorphic Adam17ex allele, were used for experimentation. Mice were housed under specific pathogen-free conditions. Experiments were approved by the Monash University Animal Ethics Committee.

extract_protocol:
Total RNA was isolated from snap-frozen mouse pancreatic tissues using TRIzol (Sigma).
Libraries were generated using an in-house multiplex RNA-seq method (MHTP, Medical Genomics Facility). Libraries were prepared using 30 ng of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. Illumina P5 was added by tagmentation by Nextera transposase and PCR and Illumina P7 was added by PCR. The library was designed so that the forward read (R1) used the standard R1 primer to sequence the cDNA in the sense direction for transcript identification. The index read (I1) used the standard i7 primer to sequence directly into the sample index and then the 10 bp UMI. Sequencing (R1 101 bp; I1 18 bp) was performed on an Illumina NextSeq 2000 using a P2 100 cycle kit, as per the manufacturer’s instructions (Life Technologies). On-board denaturing and clustering were done using 1000 pM of library pool (Illumina Protocol 1000000109376 v3 Nov2020).

treatment_protocol: The cerulein-induced mouse model of AP was established via intraperitoneal (IP) injections (1 injection per hour for 7 hours) of cerulein (50 μg/kg; Sigma, USA) or phosphate-buffered saline (PBS; 50 μl, as a control). Mice were humanely culled one hour after the last injection.

value: pancreas

value: ex/ex

value: Cerulein

value: F


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC6) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR41LC6_ID27_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC7) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR31LC7_ID28_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC5) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR17LC5_ID26_2738.AAV.PGK.GFP_Spleen


title: Adam17 ex/ex pancreas, Cerulein, replicate 3

value: M


title: Adam17 ex/ex pancreas, Cerulein, replicate 2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR91.LC4) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR91LC4_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC3) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR23LC3_ID9_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC2) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR53LC2_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC96) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR41LC96_ID24_2738.AAV.PGK.GFP_Spleen


title: Adam17 ex/ex pancreas, PBS, replicate 2

value: PBS


title: Adam17 ex/ex pancreas, Cerulein, replicate 1


title: Adam17 ex/ex pancreas, PBS, replicate 1


title: Adam17 ex/ex pancreas, PBS, replicate 3


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC1) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR31LC1_ID6_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_+P-N_rep3


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC13) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR31LC13_ID1_2738.AAV.PGK.GFP_Spleen


title: Adam17 ex/ex pancreas, PBS, replicate 4


title: WT pancreas, Cerulein, replicate 4

value: WT


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR91.LC94) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR91LC94_ID21_2738.AAV.PGK.GFP_Spleen


title: Mt_A17_+P+N_rep2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC95) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR17LC95_ID23_2738.AAV.PGK.GFP_Spleen


title: WT pancreas, Cerulein, replicate 3


title: WT pancreas, Cerulein, replicate 2


title: WT pancreas, Cerulein, replicate 1


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC92) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR53LC92_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp7 PB on NONE (LTR17.LC89) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR17LC89_UThuman_NONE_PB

value: PB


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC91) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR31LC91_ID2_2738.AAV.PGK.GFP_Spleen


title: WT pancreas, PBS, replicate 3


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC90) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR41LC90_ID1_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on NONE (LTR23.LC87) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR23LC87_ID31_NONE_Spleen


title: WT pancreas, PBS, replicate 2


title: WT pancreas, PBS, replicate 1


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC85) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR31LC85_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC84) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR41LC84_ID28_2738.AAV.PGK.GFP_Spleen


title: P0, td, 2

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

description: td' indicates the samples are from transgenic mice bred with the 'tdTomato' construct.

library_source: transcriptomic single cell

data_processing:
Processing of  scRNAseq reads was performed using the 10X Genomics Cell Ranger pipeline (v5.0.0) and visualized in R with the Seurat package (v4.0.5). Briefly, FASTQ files were generated using cellranger mkfastq with default parameters and cellranger count was run using the reference genome and annotation supplied (mm10-2.1.0) for each sample, counting UMIs for each gene. The output for each sample was integrated using cellranger aggr with default options and imported into R using Seurat for further analysis.
Assembly: mm10-2.1.0
Supplementary files format and content: *_filtered_feature_bc_matrix.h5: gene-cell barcode matrices in hdf5 format. Filtering was performed using default parameters in cellranger.

molecule: polyA RNA

source_name: BM

growth_protocol: Femurs and tibias isolated from Tie2-CreERT2;Rosa26-tdTomato mice were collected into sterile cold PBS with 2% FBS and gently crushed using a mortar and pestle. In order to avoid damaging ECs, especially those ones localized just beneath of the bones, crushing was performed very gently upon reducing each bone in 2-3 pieces. Cell suspensions were then filtered into a 50 mL tube on ice using a 70 um cell strainer while the crushed bone pieces were incubated at 37°C with gentle agitation (150 rpm) in 1-2 mL/mouse of bone digestion buffer containing DMEM supplemented with 20 mM HEPES, 3 mg/mL collagenase I, BSA 1 mg/mL, and 0.1 mg/mL DNase I. After 10 minutes, the bone digested mixture was brought to a 10 mL volume in PBS containing 2% FBS and filtered again via the 70 um cell strainer and into the 50 mL tube used previously. A further 1-2 mL of digestion media was added to the bone pieces and the mixture was incubated at 37°C in agitation (150 rpm) for additional 30 minutes. The cell suspension derived from the bone digestion was washed again in PBS with 2% FBS and added to the previous 50 mL tube after filtration through the same 70 um cell strainer on ice. The digested bone pieces were collected back into the mortar and further crushed in PBS/2% FBS. The supernatant was passed through the same 70 um cell strainer and gathered into the same 50 mL tube on ice. The whole cell suspension was centrifuged at 1200 rpm for 5 minutes and the cell pellet was dissolved in EGM-2 medium for counting.

extract_protocol: For scRNA-seq, DAPI-CD45-Ter119-tdTomato+ sorted cells from the fresh (without culture) bone marrows of two 4-month-old Tie2-CreERT2;Rosa26-tdTomato mice were loaded on the Chromium controller (10XGenomics) based on the number provided by the sorting equipment. The libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ GEM, Library & Gel Bead Kit v3 (PN-1000075), Chromium Chip B Single Cell Kit (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics) and following the Chromium Single Cell 3′ Reagent Kits (v3) User Guide (manual part no. CG000183 Rev A). Libraries were run on an Illumina HiSeq 2500 as 150-bp paired-end reads, at 20,000 read pairs per cell.

value: BM

value: primary culture

tag: passage

value: BMEC


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC83) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR17LC83_ID27_2738.AAV.PGK.GFP_Spleen

value: Spleen

value: AAV


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR91.LC82) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR91LC82_ID26_2738.AAV.PGK.GFP_Spleen


title: fresh, td, 2

value: fresh (without culture)


title: MSC, 2

data_processing:
To assess the quality of the sequencing libraries, we used the default parameters of the nf-core RNASeq pipeline, v1.4.2. Briefly, trimmed reads were mapped to the GRCm38 reference using STAR and abundance of transcripts from the Ensembl annotation (v81) was estimated using Salmon. Each library was subjected to extensive quality control, including estimation of library complexity, sequence quality, read length and depth, among other metrics detailed in the pipeline repository (https://nf-co.re/rnaseq). Pseudocounts were merged into a matrix of counts per million per gene for each sample using the tximport R package, and the resulting matrix saved as a text file.
Assembly: GRCm38, Ensembl v81
Supplementary files format and content: Expression matrix of Salmon pseudocounts, CSV

source_name: MSC

growth_protocol: WBM cells were plated on collagen type I-coated (Corning) or 0.1% gelatin (Millipore)-coated culture dishes at the density of 6-8 x 10^7/10 cm dish and started to be cultured at 37°C with 5% CO2 in an incubator (Panasonic); usually 1 mouse (2 femurs and tibias) generates 1 dish. After 2 days, half (v/v) medium was added. On day 4-5, half of cell suspension (v/v) was removed from the culture and replenished by fresh EGM-2 medium. Half (v/v) medium changes were performed every 2-3 days for approximately 2 weeks until confluent. At that point, the culture, consisting entirely of adherent cells, was gently trypsinized using 0.05% Trypsin/0.53 mM EDTA (Corning) and replated at a density of 1 x 10^6/10 cm dish. Cultures were passaged every 1-2 weeks at confluency. All passages and sorted cells from P0 were cultured for 1-2 weeks until confluent by half medium changes every 2-3 days.

extract_protocol:
Total RNAs were extracted using the Trizol reagent. Their integrity and quantity were examined using the RNA screentape on a 4200 TapeStation system (Agilent). Samples with RNA integrity number above 7 were used for library construction.
RNA-seq libraries were generated with the KAPA RNA HyperPrep Kit (Roche, no. KK8581) according to the manufacturer's protocol

tag: batch

value: c

value: MSC


title: P0 Emcn neg, 1

value: d

tag: emcn status

value: Emcn neg


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC79) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR31LC79_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC80) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR53LC80_ID9_2738.AAV.PGK.GFP_Spleen


title: Lung, 1

source_name: Lung

value: Lung


title: P0 Emcn pos, 1

value: Emcn pos


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC81) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR23LC81_ID25_2738.AAV.PGK.GFP_Spleen


title: MSC, 1


title: P3 Emcn neg, 2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC77) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR17LC77_ID24_2738.AAV.PGK.GFP_Spleen


title: WT pancreas, PBS, replicate 4

value: pancreas

tag: Sex

value: F


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC78) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR41LC78_ID6_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC93) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR23LC93_ID20_2738.AAV.PGK.GFP_Spleen


title: P2 Emcn neg, 2


title: P1 Emcn neg, 2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR53.LC74) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR53LC74_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR23.LC75) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR23LC75_ID21_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR31.LC73) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR31LC73_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR41.LC72) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR41LC72_ID2_2738.AAV.PGK.GFP_Spleen


title: P3 Emcn neg, 1

value: b


title: P1 Emcn neg, 1

value: WT


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR17.LC33) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR17LC33_ID1_2738.AAV.PGK.GFP_Spleen


title: Lung, 2

value: a


title: Exp8 Spleen on NONE (LTR19.LC38) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC38_ID30_NONE_Spleen


title: P0 Emcn neg, 2

value: BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC71) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR27LC71_ID29_2738.AAV.PGK.GFP_Spleen


title: het [N89_3_2]

city: Madrid

first: Miguel

last: Manzanares

address: Melchor Fernandez Almagro, 3

department: Cell and Developmental Biology

country: Spain

institute: National Center of Cardiovascular Diseases

description: single embryo RNA-Seq

data_processing:
Adapters were removed with Cutadapt v1.14 and sequences were mapped with Bowtie2 2.2.9 (Langmead and Salzberg, 2012) and quantified using RSEM v1.3.1 (Li and Dewey, 2011) to the transcriptome set from Mouse Genome Reference GRCm38 and Ensembl Gene Build version 98.
The corresponding genomic sequences of LacZ, Puromycin and Neomycin were added manually to our reference genome, fasta and gtf files, for in sillico genotyping.
Genome_build: mm10

source_name: blastocyst

extract_protocol: Single embryo RNAseq, CDNA synthesis was performed using SMART-Seq Ultra Low Input RNA Kit (Clontech) and Sequencing was performed using the Illumina HiSeq 2500 sequencer.

tag: sample

value: Whole blastocyst

tag: strain

tag: genotype/variation

value: het

tag: sequencing batch


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR91.LC76) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR91LC76_ID23_2738.AAV.PGK.GFP_Spleen

tag: tissue

value: Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC82) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR27LC82_ID25_2738.AAV.PGK.GFP_Spleen

value: AAV


title: het [N2_7]

description: single embryo RNA-Seq

source_name: morula

value: Whole morula


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC79) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC79_ID6_2738.AAV.PGK.GFP_Spleen


title: del [N2_4]

description: single embryo RNA-Seq

value: del


title: Exp8 PB on NONE (LTR7.LC39) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC39_UThuman_NONE_PB

value: PB


title: het [N2_5]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC80) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR77LC80_ID7_2738.AAV.PGK.GFP_Spleen


title: del [N2_3]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC78) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC78_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC40) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC40_ID28_2738.AAV.PGK.GFP_Spleen


title: P0 Emcn pos, 2

tag: genotype

tag: cell type

value: BMEC


title: P2 Emcn neg, 1

value: Emcn neg


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC77) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR3LC77_ID23_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC83) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR3LC83_ID26_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC75) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC75_ID20_2738.AAV.PGK.GFP_Spleen


title: MZKO [C50_8]

description: single embryo RNA-Seq

value: MZKO


title: het [N2_1]

description: single embryo RNA-Seq


title: MZKO [C50_6]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC74) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR77LC74_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC84) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC84_ID27_2738.AAV.PGK.GFP_Spleen


title: MZKO [C50_4]

description: single embryo RNA-Seq


title: P4 Emcn neg, 1


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC73) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC73_ID2_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC72) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC72_ID1_2738.AAV.PGK.GFP_Spleen


title: del [N2_6]

description: single embryo RNA-Seq


title: MZKO [C50_2]

description: single embryo RNA-Seq


title: Exp8 PB on NONE (LTR3.LC71) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC71_UThuman_NONE_PB


title: Exp8 Spleen on NONE (LTR77.LC68) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC68_ID30_NONE_Spleen


title: del [N2_2]

description: single embryo RNA-Seq


title: WT_flfl [N89_9]

description: single embryo RNA-Seq


title: het [N89_8]

description: single embryo RNA-Seq


title: MZKO [C50_1]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC67) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR59LC67_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC66) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR7LC66_ID28_2738.AAV.PGK.GFP_Spleen


title: WT_flfl [N89_7]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC65) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC65_ID27_2738.AAV.PGK.GFP_Spleen


title: het [N89_3]

description: single embryo RNA-Seq


title: MZ_KO [C7_7]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC61) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR59LC61_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC62) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC62_ID9_2738.AAV.PGK.GFP_Spleen


title: WT_flfl [N89_1]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC63) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR19LC63_ID25_2738.AAV.PGK.GFP_Spleen


title: MZ_KO [C7_6]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC47) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC47_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC46) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR27LC46_ID23_2738.AAV.PGK.GFP_Spleen


title: M_KO [C7_4]

description: single embryo RNA-Seq


title: M_KO [C7_5]

description: single embryo RNA-Seq


title: het [N89_5]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC45) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR19LC45_ID21_2738.AAV.PGK.GFP_Spleen


title: M_KO [C7_3]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC48) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR7LC48_ID6_2738.AAV.PGK.GFP_Spleen


title: MZKO [C50_3]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC44) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC44_ID20_2738.AAV.PGK.GFP_Spleen


title: MZ_KO [C7_2]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC43) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR59LC43_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC64) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR27LC64_ID26_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC42) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR7LC42_ID2_2738.AAV.PGK.GFP_Spleen


title: M_KO [C7_1]

description: single embryo RNA-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC41) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC41_ID1_2738.AAV.PGK.GFP_Spleen


title: het [N89_6]

description: single embryo RNA-Seq


title: E3.5_MZ KO [C89_2]

description:
C89_2_31953_CAGGCG
single embryo HiC-Seq

data_processing:
Single embryo HiC data were processed using TADbit (Serra et al., 2017) for read quality control, read mapping, interaction detection, interaction filtering, and matrix normalization.
After a FastQC protocol to discard artifacts, the remaining reads were mapped to the reference mouse genome (mm10) using a fragment-based strategy in TADbit .
After discarding non-informative contacts -including self-circles, dangling-ends, errors, random breaks or duplicates, those experiments with more than 800.000 valid-pairs were kept. Then, the experiments with the same genotype were merged and normalized.
TADs were identified by using 40-kb resolution vanilla-normalized and decay-corrected matrices as input to the TAD detection algorithm implemented in TADbit.
A–B compartments were detected by calculating the first component of a principal-component analysis (PCA) of chromosome-wide matrices (100kb) and assigning A compartments to the genomic bin with positive PCA1 values GC content. Conversely, B compartments were assigned to the genomic bin with  and high GC content.
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C matrices

source_name: E3.5_MZ KO

extract_protocol:
single embryo HiC-Seq and single embryo RNAseq
Single cell Hi-C protocol was adapted from Nagano et al., 2015, optimizing it for single embryo by scaling the reaction volumes and reducing the experimental procedures to avoid sample loss. For single embryo RNAseq, CDNA synthesis was performed using SMART-Seq Ultra Low Input RNA Kit (Clontech) and Sequencing was performed using the Illumina HiSeq 2500.

tag: strain background

value: MZ KO

tag: total reads

tag: valid-pairs

tag: restriction enzyme

value: MboI


title: E3.5_MZ KO [C95_4]

description:
C95_4_32467_CACGAT
single embryo HiC-Seq


title: Exp8 PB on NONE (LTR27.LC40) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC40_UThuman_NONE_PB

tag: vector

tag: vector id


title: Exp8 Spleen on NONE (LTR59.LC37) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC37_ID30_NONE_Spleen

tag: subject


title: E3.5_MZ KO [C72_6]

description:
C72_6_31264_GCCAAT
single embryo HiC-Seq


title: E3.5_MZ KO [C72_2]

description:
C72_2_31260_CGATGT
single embryo HiC-Seq


title: E3.5_MZ KO [C64_4]

description:
C64_4_32481_GTCCGC
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC35) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR3LC35_ID28_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC36) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC36_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC33) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR19LC33_ID26_2738.AAV.PGK.GFP_Spleen


title: E3.5_MZ KO [C61_1]

description:
C61_1_32474_CGATGT
single embryo HiC-Seq


title: E3.5_MZ KO [C61_4]

description:
C61_4_32477_TAGCTT
single embryo HiC-Seq


title: E3.5_MZ KO [C61_2]

description:
C61_2_32475_TGACCA
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC30) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC30_ID7_2738.AAV.PGK.GFP_Spleen


title: E3.5_MZ KO [C38_1]

description:
C38_1_31268_GGCTAC
single embryo HiC-Seq


title: E3.5_MZ KO [C4_6]

description:
C4_6_27301_CAGATC
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC29) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR3LC29_ID6_2738.AAV.PGK.GFP_Spleen


title: E3.5_MZ KO [C27_4]

description:
C27_4_31272_GTGGCC
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC26) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR77LC26_ID21_2738.AAV.PGK.GFP_Spleen


title: E3.5_MZ KO [C27_2]

description:
C27_2_31270_GATCAG
single embryo HiC-Seq


title: E3.5_MZ KO [C27_5]

description:
C27_5_31273_CGTACG
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC25) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC25_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC28) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC28_ID24_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C95_9]

description:
C95_9_32472_ATTCCT
single embryo HiC-Seq

source_name: E3.5_M KO

value: M KO


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC24) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC24_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC22) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC22_ID1_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on NONE (LTR37.LC69) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR37LC69_ID31_NONE_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC23) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR3LC23_ID2_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C95_8]

description:
C95_8_32471_ACTGAT
single embryo HiC-Seq


title: E3.5_M KO [C95_5]

description:
C95_5_32468_CATTTT
single embryo HiC-Seq


title: E3.5_M KO [C72_5]

description:
C72_5_31263_ACAGTG
single embryo HiC-Seq


title: E3.5_M KO [C95_3]

description:
C95_3_32466_AGTCAA
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR51.LC71) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR51LC71_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC34) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC34_ID27_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C72_4]

description:
C72_4_31262_TGACCA
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC32) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR77LC32_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC83) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR29LC83_ID26_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C64_6]

description:
C64_6_32483_ATGAGC
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR51.LC80) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR51LC80_ID7_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C4_8]

description:
C4_8_27303_TAGCTT
single embryo HiC-Seq


title: E3.5_M KO [C4_7]

description:
C4_7_27302_GATCAG
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC79) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR57LC79_ID6_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR87.LC81) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR87LC81_ID9_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C4_2]

description:
C4_2_27297_CGATGT
single embryo HiC-Seq


title: E3.5_M KO [C4_5]

description:
C4_5_27300_GCCAAT
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC78) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR35LC78_ID24_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C27_3]

description:
C27_3_31271_GTGAAA
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR51.LC74) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR51LC74_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR87.LC75) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR87LC75_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC76) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR37LC76_ID21_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE36]

description:
SE36_32464_CCAACA
single embryo HiC-Seq


title: E3.5_WT [SE32]

description:
SE32_32484_CACTCA
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC73) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR57LC73_ID2_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE25]

description:
SE25_24082_ACTGAT
single embryo HiC-Seq


title: E3.5_WT [SE3]

description:
SE3_23901_CCGTCC
single embryo HiC-Seq


title: E3.5_M KO [C72_3]

description:
C72_3_31261_TTAGGC
single embryo HiC-Seq


title: Exp7 Spleen on NONE (LTR87.LC69) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR87LC69_ID31_NONE_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC72) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR35LC72_ID1_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE2]

description:
SE2_23900_AGTTCC
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC67) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR57LC67_ID29_2738.AAV.PGK.GFP_Spleen


title: E3.5_M KO [C64_5]

description:
C64_5_32482_GTTTCG
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC82) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR37LC82_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC40) rep 3

description:
AAV_AAVS1.tsv
Exp7_LTR57LC40_ID28_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE16]

description:
SE16_31265_CCGTCC
single embryo HiC-Seq


title: E3.5_WT [SE23]

description:
SE23_24081_GAGTGG
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC65) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR29LC65_ID27_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC66) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR35LC66_ID28_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE15]

description:
SE15_31266_ATGTCA
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC64) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR37LC64_ID26_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE12]

description:
SE12_27305_CTTGTA
single embryo HiC-Seq


title: E3.5_WT [SE11]

description:
SE11_27304_GGCTAC
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC48) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR35LC48_ID6_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC47) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR29LC47_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp8 PB on NONE (LTR7.LC31) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC31_UThuman_NONE_PB


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR87.LC63) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR87LC63_ID25_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE1]

description:
SE1_23899_AGTCAA
single embryo HiC-Seq


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC46) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR37LC46_ID23_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE14]

description:
SE14_27295_AGTTCC
single embryo HiC-Seq


title: Exp8 Spleen on NONE (LTR19.LC28) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC28_ID30_NONE_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR51.LC44) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR51LC44_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC27) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR77LC27_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC25) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC25_ID27_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC41) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR29LC41_ID1_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC26) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC26_ID28_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC23) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR27LC23_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC42) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR35LC42_ID2_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC61) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR57LC61_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on NONE (LTR51.LC38) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR51LC38_ID31_NONE_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC43) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR57LC43_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC34) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR37LC34_ID27_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC22) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC22_ID9_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC36) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR35LC36_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC24) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR3LC24_ID26_2738.AAV.PGK.GFP_Spleen


title: E3.5_WT [SE13]

description:
SE13_27294_AGTCAA
single embryo HiC-Seq


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC21) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR77LC21_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC20) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC20_ID6_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC35) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR29LC35_ID28_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR87.LC33) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR87LC33_ID26_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR51.LC32) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR51LC32_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC18) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR3LC18_ID23_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC19) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR7LC19_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC16) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR19LC16_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC30) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR35LC30_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC29) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR29LC29_ID6_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC15) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR77LC15_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC28) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR37LC28_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC14) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR59LC14_ID2_2738.AAV.PGK.GFP_Spleen


title: Exp8 PB on NONE (LTR3.LC12) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC12_UThuman_NONE_PB


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR87.LC27) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR87LC27_ID23_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on NONE (LTR77.LC9) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC9_ID30_NONE_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR51.LC26) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR51LC26_ID21_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC7) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR7LC7_ID28_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC8) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR59LC8_ID29_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC25) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR57LC25_ID20_2738.AAV.PGK.GFP_Spleen


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR37.LC22) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR37LC22_ID1_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC5) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR27LC5_ID26_2738.AAV.PGK.GFP_Spleen


title: liver, LPS-input, rep3

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: No. 6, Tongwei Road, Xuanwu District

department: College of Animal Science and Technology

country: China

institute: Nanjing Agricultural University

data_processing:
library strategy: meRIP-seq
paired-end reads were harvested from the Illumina NovaSeq 6000 sequencer, and Q30 scoring was used for quality control
Fasqtc (v0.11.5) and Cutadapt software (v1.9.3) was employed for 3′-adaptor_x0002_trimming and removal of low-quality reads. The clean reads were aligned to the reference pig genome sequences (galGal6) using Hisat2 software
The m6A_x0002_modification peaks were called by MACS software, the “effective genome size” parameter was adjusted to the calculated transcriptome size (1.77 x 108)
Line-dynamic methylated peaks,which showing a change of intensity in some of the common peaks, were identified by diffReps software
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

organism: Sus scrofa

source_name: liver

extract_protocol:
Total RNA was extracted with TRIZol reagent. Polyadenylated RNA was enriched by using PolyATtract® mRNA Isolation System III.Partial mRNA samples were saved as input control. A total of 5 µg fragmented mRNA was incubated with 12 µg anti-m6A antibody. Both the m6A IP samples and the input samples without IP were used for library generation with NEBNext® Ultra II Directional RNA Library Prep Kit.
IP of the m6A RNA was performed with the GenSeqTM m6A RNA IP Kit following the manufacturer’s instructions.

treatment_protocol: piglets in the LPS group received intraperitoneal injection with 80 ug/kg LPS, while the remaining piglets in the CON group were given an equal dose of sterile saline.

value: liver

value: male

value: Duroc x Large White x Landrace

tag: treatment

value: LPS


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR44.LC10) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR44LC10_A004_2733.IDLV.PGK.GFP_BM

source_name: IDLV PGK GFP

value: BM

value: IDLV


title: liver, LPS-input, rep2


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR42.LC9) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR42LC9_A002_2733.IDLV.PGK.GFP_BM


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR57.LC31) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR57LC31_ID9_2738.AAV.PGK.GFP_Spleen

value: Spleen


title: liver, LPS-input, rep1


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC17) rep 3

description:
AAV_AAVS1.tsv
Exp8_LTR27LC17_ID21_2738.AAV.PGK.GFP_Spleen

value: AAV


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC2) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR59LC2_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp9 PB on NONE (LTR38.LC7) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR38LC7_UThuman_NONE_PB


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR36.LC6) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR36LC6_A004_2733.IDLV.PGK.GFP_BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC1) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR7LC1_ID6_2738.AAV.PGK.GFP_Spleen


title: liver, control-input, rep3

value: sterile saline


title: Left-right 15 [y15]

city: Menlo Park

first: Adam

last: Knight

state: CA

address: 1305 Obrien Dr

institute: pacbio

data_processing:
demultiplex with Lima
isoseq 3.0
mapped full length transcripts with minmap2
counted transcript hits to reference transcriptome from SAM file
Assembly: TBD
Supplementary files format and content: counts.txt

organism: Patiria miniata

source_name: sectioned from whole arm

extract_protocol:
RNA extracted using qiagen RNAeasy and modified Trizol protocol
Iso-Seq Express Template Preparation protocol / SMRTbell Express Template Prep Kit 2.0

treatment_protocol: arm embedded in HistoPrep medium and cryosectioned using Leica CM3050-S microtome

value: sectioned from whole arm

tag: isolate

value: specimen 2


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR35.LC24) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR35LC24_ID3_2738.AAV.PGK.GFP_Spleen


title: liver, control-input, rep2-2

tag: Sex


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR87.LC45) rep 2

description:
AAV_AAVS1.tsv
Exp7_LTR87LC45_ID21_2738.AAV.PGK.GFP_Spleen


title: Left-right 16 [y16]


title: Exp7 Spleen on 2738.AAV.PGK.GFP (LTR29.LC23) rep 1

description:
AAV_AAVS1.tsv
Exp7_LTR29LC23_ID2_2738.AAV.PGK.GFP_Spleen


title: Exp9 PB on NONE (LTR30.LC3) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR30LC3_UThuman_NONE_PB

value: PB


title: Left-right 14 [y14]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC95) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR27LC95_ID23_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC96) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC96_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp9 PB on NONE (LTR46.LC11) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR46LC11_UThuman_NONE_PB


title: liver, control-input, rep2-1


title: liver, control-input, rep1-2


title: Left-right 13 [y13]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC94) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR19LC94_ID21_2738.AAV.PGK.GFP_Spleen


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR26.LC1) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR26LC1_A002_2733.IDLV.PGK.GFP_BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC4) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR19LC4_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC93) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR77LC93_ID20_2738.AAV.PGK.GFP_Spleen


title: liver, control-input, rep1-1


title: Left-right 12 [y12]


title: Exp10 PB on NONE (LTR33.LC95) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR33LC95_UThuman_NONE_PB


title: Left-right 11 [y11]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC92) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR59LC92_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR34.LC5) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR34LC5_A002_2733.IDLV.PGK.GFP_BM


title: liver, LPS-IP, rep2


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR83.LC94) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR83LC94_A004_2733.IDLV.PGK.GFP_BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC91) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR7LC91_ID2_2738.AAV.PGK.GFP_Spleen


title: Left-right 10 [y10]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR15.LC93) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR15LC93_A002_2733.IDLV.PGK.GFP_BM


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR28.LC2) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR28LC2_A004_2733.IDLV.PGK.GFP_BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC90) rep 2

description:
AAV_AAVS1.tsv
Exp8_LTR3LC90_ID1_2738.AAV.PGK.GFP_Spleen


title: Exp10 PB on NONE (LTR73.LC91) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR73LC91_UThuman_NONE_PB


title: Left-right 9 [y09]


title: liver, LPS-IP, rep1


title: liver, control-IP, rep3-2


title: Exp8 PB on NONE (LTR27.LC89) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC89_UThuman_NONE_PB


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR81.LC90) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR81LC90_A004_2733.IDLV.PGK.GFP_BM


title: Left-right 8 [y08]


title: Left-right 7 [y07]


title: liver, control-IP, rep3-1


title: Exp8 Spleen on NONE (LTR59.LC86) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC86_ID30_NONE_Spleen


title: liver, control-IP, rep2


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC85) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC85_ID29_2738.AAV.PGK.GFP_Spleen


title: Left-right 6 [y06]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR33.LC89) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR33LC89_A002_2733.IDLV.PGK.GFP_BM


title: liver, LPS-IP, rep3


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC84) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR3LC84_ID28_2738.AAV.PGK.GFP_Spleen


title: Left-right 5 [y05]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC83) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC83_ID27_2738.AAV.PGK.GFP_Spleen


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR9.LC86) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR9LC86_A004_2733.IDLV.PGK.GFP_BM


title: liver, control-IP, rep1


title: Exp10 PB on NONE (LTR15.LC87) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR15LC87_UThuman_NONE_PB


title: Left-right 4 [y04]


title: CCEx11_B19_1_dense_S_vbc

city: Boston

first: Arpiar

last: Saunders

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
CCEx11
single-cell RNA profiling using 3' counting

data_processing:
Sequencing was performed on either an Illumina MiSeq, NextSeq 500 or NovaSeq6000
Sequencing Reads were aligned against a custom genome containing the GRCm38.81 mouse build; the rabies virus genome (SAD-B19-dG-EGFP) and AAV elements using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output. Columns belong to STAMPs (cells) and transcript counts (rows)
Viral barcodes (VBCs) were amplified from sequenced EGFP mRNAs. Raw VBC sequences ascertained from viral genomes or scRNA-seq data (RM) were collapsed (RB) using custom algorithms. UMIs were used count/collapse VBC sequences within the context of a cell (XC)
Assembly: GRCm38.81 + custom genomes for SAD-B19-dG-EGFP and AAV elements
Supplementary files format and content: digital gene expression

source_name: Cortex Culture + FACS for starter cells (mCherry+/EGFP+) Experiment 11, SBARRO (Infected by AAVs & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx11_B19_1_dense_S_vbc]

extract_protocol:
Saunders and Macosko et al. 2018 Cell
10x Genomics 3' RNA (v2 or v3 chemistry) & this study (for viral barcode processing/sequencing)
10x Genomics 3' RNA & this study (for viral barcode processing/sequencing)

treatment_protocol: Cells were dissociated from in vitro synaptic cultures, FACS to enrich for those cells infected by rabies virus and scRNA-seq libraries were generated using 10x Genomic v2 or v3 platforms


title: CCEx11_B19_1_dense_P_vbc

source_name: Cortex Culture + FACS for presynaptic cells (mCherry-/EGFP+) Experiment 11, SBARRO (Infected by AAVs & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx11_B19_1_dense_P_vbc]


title: Left-right 3 [y03]


title: Left-right 2 [y02]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC81) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR77LC81_ID25_2738.AAV.PGK.GFP_Spleen


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR45.LC82) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR45LC82_A004_2733.IDLV.PGK.GFP_BM


title: Exp10 PB on NONE (LTR67.LC83) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR67LC83_UThuman_NONE_PB


title: CCEx16_B19_noRG_1in100x_L3_vbc

description:
CCEx16
single-cell RNA profiling using 3' counting

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 3. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 100) [CCEx16_B19_noRG_1in100x_L3_vbc]


title: CCEx16_B19_noRG_1in100x_L2_vbc

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 2. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 100) [CCEx16_B19_noRG_1in100x_L2_vbc]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC80) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC80_ID9_2738.AAV.PGK.GFP_Spleen


title: Oral-aboral 8 [z08]

value: specimen 1


title: CCEx16_B19_noRG_1in100x_L1_vbc

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 100) [CCEx16_B19_noRG_1in100x_L1_vbc]


title: Exp10 PB on NONE (LTR79.LC79) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR79LC79_UThuman_NONE_PB

source_name: Untransduced


title: Left-right 1 [y01]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR95.LC81) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR95LC81_A002_2733.IDLV.PGK.GFP_BM


title: CCEx16_B19_noRG_1in10x_L2_vbc

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 2. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx16_B19_noRG_1in10x_L2_vbc]


title: Oral-aboral 7 [z07]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR75.LC78) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR75LC78_A004_2733.IDLV.PGK.GFP_BM


title: Oral-aboral 6 [z06]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC82) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR19LC82_ID26_2738.AAV.PGK.GFP_Spleen

source_name: AAV PGK GFP


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC77) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC77_ID24_2738.AAV.PGK.GFP_Spleen


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR67.LC77) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR67LC77_A002_2733.IDLV.PGK.GFP_BM


title: CCEx16_B19_noRG_1in10x_L1_vbc

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx16_B19_noRG_1in10x_L1_vbc]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR73.LC85) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR73LC85_A002_2733.IDLV.PGK.GFP_BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR19.LC76) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR19LC76_ID23_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC78) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR3LC78_ID6_2738.AAV.PGK.GFP_Spleen


title: CCEx16_B19_noRG_1x_L2_vbc

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 2. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = none) [CCEx16_B19_noRG_1x_L2_vbc]


title: Exp10 PB on NONE (LTR95.LC75) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR95LC75_UThuman_NONE_PB


title: Oral-aboral 4 [z04]


title: CCEx16_B19_noRG_1x_L1_vbc

source_name: Cortex Culture No RV Glycoprotein Experiment 16, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = none) [CCEx16_B19_noRG_1x_L1_vbc]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR5.LC74) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR5LC74_A004_2733.IDLV.PGK.GFP_BM


title: Oral-aboral 3 [z03]


title: CCEx15_B19_noRG_1x_L1_vbc

description:
CCEx15
single-cell RNA profiling using 3' counting

source_name: Cortex Culture No RV Glycoprotein Experiment 15, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = none) [CCEx15_B19_noRG_1x_L1_vbc]


title: CCEx12_B19_noRG_1in10x_L1_vbc

description:
CCEx12
single-cell RNA profiling using 3' counting

source_name: Cortex Culture No RV Glycoprotein Experiment 12, Library 1. SBARRO (Infected by AAVs CAG-Flex-TCB + Syn1-EBFP-Cre & EnvA-RVdG-EGFP-VBC. RV dilution factor = 1 in 10) [CCEx12_B19_noRG_1in10x_L1_vbc]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR77.LC75) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR77LC75_ID21_2738.AAV.PGK.GFP_Spleen


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR79.LC73) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR79LC73_A002_2733.IDLV.PGK.GFP_BM


title: Oral-aboral 2 [z02]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC79) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC79_ID7_2738.AAV.PGK.GFP_Spleen


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR53.LC70) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR53LC70_A004_2733.IDLV.PGK.GFP_BM


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR7.LC73) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR7LC73_ID3_2738.AAV.PGK.GFP_Spleen


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR3.LC72) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR3LC72_ID2_2738.AAV.PGK.GFP_Spleen


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR31.LC69) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR31LC69_A002_2733.IDLV.PGK.GFP_BM


title: Oral-aboral 1 [z01]


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR27.LC33) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR27LC33_ID1_2738.AAV.PGK.GFP_Spleen


title: SCC08_1e-3_F_L2_vbc

description:
SCC08
single-cell RNA profiling using 3' counting

source_name: Striatal-Cortex Co-Culture Experiment 8, Well F, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_F_L2_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR91.LC66) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR91LC66_A004_2733.IDLV.PGK.GFP_BM


title: SCC08_1e-3_D_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well D. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_D_vbc]


title: Proximo-distal 22 [x22]


title: TS89_06_KD_3

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

description: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).

data_processing:
Reads were aligned to the human genome (GRCh38 and gene annotated with its corresponding GTF files (GENCODE GRCh38) using STAR version 2.4.2a with the settings --outFilterMultimapNmax 20 ,--outFilterType BySJout, --alignSJoverhangMin 8, --quantMode GeneCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: THP1 cells

extract_protocol:
Total RNA was extracted from NTC or HMG20B KD THP1 cells using QIAshredder spin columns and an RNeasy Plus Micro Kit (Qiagen, Manchester, UK) and its quality confirmed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: knockdown


title: SCC08_1e-3_E_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well E. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_E_vbc]

tag: strain


title: Oral-aboral 5 [z05]

source_name: sectioned from whole arm


title: Proximo-distal 21 [x21]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR23.LC65) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR23LC65_A002_2733.IDLV.PGK.GFP_BM

source_name: IDLV PGK GFP


title: Proximo-distal 20 [x20]


title: SCC08_1e-3_C_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well C. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_C_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR41.LC62) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR41LC62_A004_2733.IDLV.PGK.GFP_BM


title: TS89_05_KD_2

growth_protocol: Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).


title: TS89_04_KD_1


title: Exp8 Spleen on 2738.AAV.PGK.GFP (LTR59.LC74) rep 1

description:
AAV_AAVS1.tsv
Exp8_LTR59LC74_ID20_2738.AAV.PGK.GFP_Spleen


title: Proximo-distal 19 [x19]


title: SCC08_1e-3_A_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_A_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR57.LC58) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR57LC58_A004_2733.IDLV.PGK.GFP_BM


title: SCC08_1e-3_B_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B. SBARRO (nfected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_B_vbc]


title: Proximo-distal 18 [x18]


title: TS89_03_NTC_3

value: non-targeting control (NTC)


title: TS89_02_NTC_2


title: SCC08_1e-3_F_L1_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well F, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC08_1e-3_F_L1_vbc]


title: Proximo-distal 17 [x17]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR35.LC57) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR35LC57_A002_2733.IDLV.PGK.GFP_BM


title: SCC08_1e-2_B_L3_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L3_vbc]


title: Proximo-distal 16 [x16]


title: TS89_01_NTC_1


title: SCC08_1e-2_B_L2_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L2_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR87.LC54) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR87LC54_A004_2733.IDLV.PGK.GFP_BM


title: Proximo-distal 15 [x15]


title: TS81_4_4_KD_H3K27_S4

description:
Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).
Human THP1 AML cells were infected with a lentivirus targeting HMG20B for KD or a non-targeting control (NTC) and selected using puromycin. Cells were subjected to ChIP-sequencing for LSD1, GFI1, HMG20B and H3K27ac four days upon KD.

data_processing:
Reads were aligned to the human genome (hg38) using BWA-MEM v0.7.15 (5). Reads were further filtered using Bedtools v2.25.0 to keep only reads that mapped to standard chromosomes and to remove reads mapped to blacklisted regions defined by ENCODE (http://mitra.stanford.edu/kundaje).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

extract_protocol:
10^8 cells were used for each precipitation using the method described by Lee et al. (2006). Briefly, cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature before the reaction was quenched with 0.125M glycine. Cell pellets were washed twice with PBS and nuclear lysates sonicated for 6 cycles using a Bioruptor® Pico (Diagenode, Liege, Belgium). 10μg of antibody bound to 100μl of magnetic beads (Dynabeads Protein G, Invitrogen, Carlsbad, CA) was added to each sample and immunoprecipitation performed overnight on a rotator at 4°C and 20rpm. After five washes with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl), chromatin IP-bound fractions were extracted by incubating for 15 min at 65°C with elution buffer (50mM TrisHCl pH8, 10mM EDTA, 1% SDS). Crosslinking was then reversed by incubation at 65°C for 6 hours. RNaseA (1mg/ml) and proteinase K (20mg/ml) were added to eliminate RNA and protein from the samples. DNA was extracted using phenol:chloroform:isoamyl alcohol and precipitated by adding 2 volumes of ice-cold 100% ethanol, glycogen (20μg/μl), 200mM NaCl and freezing at -80°C for at least 1hr. Pellets were washed with 70% ethanol and eluted in 50μl 10mM TrisHCl pH8.0.
Libraries were prepared for sequencing using a Microplex Library Preparation Kit (Diagenode). 200-800bp fragments were selected using AMPure beads (Beckman Coulter, Brea, CA) and quantified by qPCR with a KAPA Library Quantification Kit (Kapa Biosystems, Basel, Switzerland). Sequencing was performed using a NextSeq desktop sequencing system (Illumina) with 75bp, paired-end high output generating 65-80M reads per sample.

tag: chip antibody

value: anti-acetyl-H3K27 (ab4729; Abcam)


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR51.LC53) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR51LC53_A002_2733.IDLV.PGK.GFP_BM

tag: tissue


title: SCC08_1e-2_B_L1_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well B, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_B_L1_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR17.LC61) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR17LC61_A002_2733.IDLV.PGK.GFP_BM


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR29.LC50) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR29LC50_A004_2733.IDLV.PGK.GFP_BM


title: SCC08_1e-2_A_L3_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L3_vbc]


title: Proximo-distal 13 [x13]


title: TS81_3_3_KD_HMG20B_S3

value: anti-HMG20B (ab72302; Abcam)


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR37.LC49) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR37LC49_A002_2733.IDLV.PGK.GFP_BM


title: SCC08_1e-2_A_L2_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L2_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR20.LC46) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR20LC46_A001_2733.IDLV.PGK.GFP_BM


title: Proximo-distal 12 [x12]


title: SCC08_1e-2_A_L1_vbc

source_name: Striatal-Cortex Co-Culture Experiment 8, Well A, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC08_1e-2_A_L1_vbc]


title: TS81_1_1_KD_LSD1_S1

value: anti-LSD1 (ab17721; Abcam)


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR18.LC45) rep 3

description:
IDLV_AAVS1.tsv
Exp9_LTR18LC45_A000_2733.IDLV.PGK.GFP_BM


title: Proximo-distal 11 [x11]


title: SCC07_1e-3_E_vbc

description:
SCC07
single-cell RNA profiling using 3' counting

source_name: Striatal-Cortex Co-Culture Experiment 7, Well E. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_E_vbc]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR12.LC42) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR12LC42_A001_2733.IDLV.PGK.GFP_BM


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR10.LC41) rep 2

description:
IDLV_AAVS1.tsv
Exp9_LTR10LC41_A000_2733.IDLV.PGK.GFP_BM


title: TS80_2_NTC_GFI1_S4

value: anti-GFI1 (ab21061; Abcam)


title: Proximo-distal 10 [x10]


title: Proximo-distal 9 [x09]


title: TS80_3_NTC_HMG20B_S3


title: SCC07_1e-3_D_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well D. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_D_vbc]


title: Proximo-distal 8 [x08]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR4.LC38) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR4LC38_A001_2733.IDLV.PGK.GFP_BM


title: TS80_1_NTC_LSD1_S1


title: Proximo-distal 14 [x14]


title: SCC07_1e-3_C_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_C_vbc]


title: TS38_6_LSD1_ZNF_HMG_og86

description:
Cultured in RPMI 1640 medium (Sigma Aldrich) supplemented with 2mM L-Glutamine (Life Technologies) and 10% fetal bovine serum (Sigma Aldrich).
Human THP1 AML cells were infected with lentivirus to induce doxycycline-induced expression of Flag-tagged full HMG20B, or a fusion protein containing the GFI1 DNA binding domain (GFI1-ZNF) fused with the full HMG20B. Cells were grown in the presence or absence of doxycycline for 48 hr. and subsequently ChIP-sequencing for LSD1, GFI1, Flag-HMG20B/GFI1-ZNF-HMG20B or H3K27ac was done.

source_name: THP1 cells

value: Flag (F3165; Sigma)


title: Proximo-distal 7 [x07]


title: Exp9 BM on 2733.IDLV.PGK.GFP (LTR2.LC37) rep 1

description:
IDLV_AAVS1.tsv
Exp9_LTR2LC37_A000_2733.IDLV.PGK.GFP_BM


title: SCC07_1e-3_B_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_B_vbc]


title: TS38_5_LSD1_ZNF_HMG_dmso


title: Proximo-distal 6 [x06]

source_name: sectioned from whole arm


title: TS81_2_2_KD_GFI1_S2


title: SCC07_1e-3_A_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well A. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_A_vbc]


title: Proximo-distal 5 [x05]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR15.LC33) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR15LC33_A000_2733.IDLV.PGK.GFP_BM

source_name: IDLV PGK GFP


title: TS38_4_Flag_ZNF_HMG_og86


title: SCC07_1e-3_F_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well F. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-3) [SCC07_1e-3_F_vbc]


title: TS80_4_NTC_H3K27ac_S2


title: Proximo-distal 4 [x04]


title: SCC07_1e-2_C_L4_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 4. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L4_vbc]


title: TS38_3_Flag_ZNF_HMG_dmso


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR81.LC30) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR81LC30_A001_2733.IDLV.PGK.GFP_BM


title: SCC07_1e-2_C_L3_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L3_vbc]


title: TS38_2_Flag_HMG20_og86


title: SCC07_1e-2_C_L2_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L2_vbc]


title: TS38_1_Flag_HMG20B_dmso


title: Proximo-distal 3 [x03]


title: Proximo-distal 2 [x02]


title: SCC07_1e-2_C_L1_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well C, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_C_L1_vbc]


title: Proximo-distal 1 [x01]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR9.LC26) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR9LC26_A001_2733.IDLV.PGK.GFP_BM


title: Colo829_THZ531_rep3

city: Montreal

first: Philippe

middle: P.

last: Roux

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cance

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.7.1a
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 32 transcript annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

growth_protocol: A375 and Colo829 were respectively maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 4.5 g/liter glucose and in Roswell Park Memorial Institute Medium (RPMI), supplemented with 10% fetal bovine serum, 100 IU/mL penicillin and 100 µg/mL streptomycin under 37°C/5%CO2 condition.

extract_protocol:
TriZol +  RNeasy mini kit (Qiagen)
Kapa RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific)

treatment_protocol: Melanoma cell line were treated during 6 hours with DMSO or THZ531 at 500 nM

tag: cancer

value: melanoma cell line


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR83.LC34) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR83LC34_A001_2733.IDLV.PGK.GFP_BM


title: SCC07_1e-2_B_L4_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 4. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L4_vbc]


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR73.LC25) rep 1

description:
IDLV_AAVS1.tsv
Exp10_LTR73LC25_A000_2733.IDLV.PGK.GFP_BM


title: Colo829_THZ531_rep2


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR45.LC22) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR45LC22_A001_2733.IDLV.PGK.GFP_BM


title: SCC07_1e-2_B_L3_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 3. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L3_vbc]


title: isw1∆Tm

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
NOT PROVIDED; REQUESTED
Assembly: R64
Supplementary files format and content: Bigwig files providing coverage for all samples. All values are normalized to total number of reads.

organism: Saccharomyces cerevisiae

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For ER stress induction , tunicmycin (Tm) was added to a final concentration of 1 µg/ml for 2 H .

extract_protocol: Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript.

treatment_protocol: Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3). Cells were broken and extracts were prepared as described in the original publication.

tag: cell type

tag: genotype

value: 1 µg/ml tunicamycin for 2 H

tag: molecule subtype

value: Rpb1 immunoprecipitated nascent RNA


title: SCC07_1e-2_B_L2_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 2. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L2_vbc]


title: isw1∆Untreated

value: Mat a leu2-3,112 trp1-1 can1-100 ura3-1 ade2-1 his3-11,15, RPB1-HTP::TRP, ISW1::KanMx

value: Untreated (Standard growth conditions)


title: Colo829_Ctl_rep3


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR95.LC21) rep 3

description:
IDLV_AAVS1.tsv
Exp10_LTR95LC21_A000_2733.IDLV.PGK.GFP_BM

value: BM

value: IDLV


title: Colo829_THZ531_rep1


title: SCC07_1e-2_B_L1_vbc

source_name: Striatal-Cortex Co-Culture Experiment 7, Well B, Library 1. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-2) [SCC07_1e-2_B_L1_vbc]


title: WTUntreated

source_name: wild-type

value: wild-type


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR67.LC17) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR67LC17_A000_2733.IDLV.PGK.GFP_BM


title: Colo829_Ctl_rep2


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR33.LC29) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR33LC29_A000_2733.IDLV.PGK.GFP_BM


title: Exp10 BM on 2733.IDLV.PGK.GFP (LTR75.LC18) rep 2

description:
IDLV_AAVS1.tsv
Exp10_LTR75LC18_A001_2733.IDLV.PGK.GFP_BM


title: SCC06_1e-4_C_vbc

description:
SCC06
single-cell RNA profiling using 3' counting

source_name: Striatal-Cortex Co-Culture Experiment 6, Well C. SBARRO (Infected by AAVs &  EnvA-RVdG-EGFP-VBC. Cre dilution  = 1e-4) [SCC06_1e-4_C_vbc]