title: Zic3-ChIP-seq-24h-dox

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Zic3 is dox-inducible

extract_protocol: Truseq ChIP Library Preparation kit (Illumina)

tag: target-protein

tag: chip antibody

value: Rabbit anti-HA (cat:ab9110, Abcam, ChIP-grade)


title: HCT116 FLAG-HA-RBM33 replicate A FLAG immunoprecipitation

status: Public on May 18 2022

type: SRA

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Adapters were trimmed using Cutadapt v3.1
UMI information for each read was extracted using UMI-tools v1.1.2
Pseudogenes of NORAD were masked from the reference genome GRCh38, and reads were mapped to the masked genome using STAR v2.7.1a
PCR duplicates were marked based on UMI information using UMI-tools and removed. Only uniquely mapped reads were used for the following analyses
Annotation of the transcripts were based on GENCODE v30
Read depth was calculated for each genomic position using Samtools v1.10
Normalized reads per million (PRM) was calculated using an in-house script
Genome_build: hg38
Supplementary_files_format_and_content: NA

molecule: total RNA

organism: Homo sapiens

source_name: HCT116 colon cancer cell line

growth_protocol: Cell lines were obtained from ATCC. HCT116 cells (male) were cultured in McCoy’s 5A media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Gibco, Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco). 293T cells were cultured in DMEM media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Gibco, Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco)

extract_protocol:
anti-FLAG-M2 immunoprecipitation of crosslinked RNAs
Custom library
eCLIP

treatment_protocol: 250 nm UV irradiation 400 mJ/cm2

tag: transfection

value: FLAG-HA-RBM33 transfected

tag: replicate

value: A

tag: input/ip

value: IP


title: Input-24-dox-Zic3-3HA

city: Brussels

first: Cedric

last: Blanpain

state: anderlecht

address: Route de Lennik 808, Bat C, C6-126

country: Belgium

institute: Université Libre de Bruxelles (ULB)

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Pluripotent stem cells were differentiated using published hanging drop protocols (1000 initial cells in serum-condtining medium)

treatment_protocol: Doxycycline was added to induce the expression of Mesp1 or Zic3

value: Input

tag: time

tag: condition

value: dox

tag: cell type

value: embryonic pluripotent stem cells


title: Shrew218Kidney

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression

organism: Blarina brevicauda

source_name: Kidney

growth_protocol: Wild caught

extract_protocol:
Tissues were extracted from recently (<12hr) deceased or euthanized animals and flash frozen in liquid nitrogen. Animals not euthanized in lab were kept at 4°C and processed within 12hr of death. Frozen tissues were pulverized using a Cell Crusher piston chilled with liquid nitrogen to produce uniform powdered tissue. Approximately 30mg of frozen tissue powder was used for Trizol RNA extraction. Contaminating DNA was removed from RNA samples using Purelink DNase kit along with Purelink RNA columns. Purified RNA quality was checked using agarose gel examination for rRNA integrity and Qubit analysis
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
Ribo-depletion for RNAseq

treatment_protocol: No treatment

tag: tissue

value: Kidney


title: M1_IP

city: Shanghai

first: Congshan

last: Liu

address: 207 Rui Jin Er Road

country: China

institute: National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention

data_processing:
Fastq files for male and female mosquitoes were trimmed using Fastp software
RNA-seq data from control mRNA and m6A mRNA were mapped to Anopheles sinensis reference genome sequence (Version: v49) using HISAT2 package
Mapped reads of IP and input cDNA libraries from male and female mosquitoes were used to identify peaks by R package exomePeak
The m6A peaks were annotated using R package ChIPseeker and visualized using IGV software
The read counts per gene were then normalized to obtain FPKM values (total exon fragments /mapped reads (millions) × exon length (kB)) using StringTie
Genome_build: Anopheles sinensis reference genome sequence (Version: v49)
Supplementary_files_format_and_content: peak text files

molecule: polyA RNA

organism: Anopheles sinensis

source_name: Anopheles sinensis

extract_protocol:
Total RNA of male and female adult Anopheles sinensis was extracted separately using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. The Poly (A) RNA was purified from 200 μg total RNA using one round Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: adult

tag: Sex

value: male

tag: m6a antibody

value: No.202003, Synaptic Systems, Germany


title: HCT116 FLAG-HA-RBM33 replicate A input


title: ATAC-seq-Zic3-KO-24h-dox

data_processing:
Quality filtering using trimmomatic
Alignment using bowtie2
Quality filtering using samtools and picard tools
Peak calling using Macs2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

extract_protocol: Nextera DNA sample Preparation Kit

treatment_protocol: Doxycycline was added to induce the expression of Mesp1

tag: genotype


title: M1_input


title: HCT116 FLAG-HA-RBM33 replicate B input

value: B


title: M2_input


title: Cth-infected YL-12

city: Nashville

first: Keith

middle: T

last: Wilson

state: TN

address: 2215B Garland Ave., 1015B MRB IV

institute: Vanderbilt University Medical Center

description: Cth-infected

data_processing:
Reads were trimmed of the adapter sequences and read quality was checked using fastp
Reads were mapped to the indexed transcriptome of the GRCm38 assembly and quantified using Salmon
Transcript-level quantification was summarized to the gene-level using tximeta
Raw transcript counts were determined using the R package DESeq2. Genes that had a sinlge count or less across samples were excluded
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts of each gene for each sample

source_name: F4/80+ gastric macrophages

growth_protocol: Age-matched (8-12 weeks) male and female C57BL/6 and C57BL/6 Cth–/– mice were house/bred in our animal facility.

extract_protocol:
Total RNA was isolated using the RNeasy Micro kit (Qiagen).
Total RNA was amplified using the Ovation RNA-Seq System V2 (Nugen) followed but librabry preparation using the NEBNext® Poly(A) selection RNA Library Prep Kit for Illumina® (BioLabs, Inc.)

treatment_protocol: Mice were gavaged on day 0 and day 2 with 1x10^9 H. pylori strain SS1. Stomachs were harvested after 16 weeks and gastric macrophages were isolated using F4/80 positive selection

tag: infected

value: Yes

value: Cth-/-


title: HCT116 empty vector control replicate B FLAG immunoprecipitation

value: Empty vector transfected


title: Shrew218Heart

source_name: Heart

value: Heart


title: F3_IP

value: female


title: Shrew217Skin

source_name: Skin

value: Skin


title: RNA-seq_batch2_WT_0h_rep1

data_processing:
Quality filtering using Trimmomatic
alignment using STAR
Read counting in genes using HT-seq count
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: count_file

extract_protocol: Qiagen RNA extraction kit

value: WT


title: ATAC-seq-Zic2-3-dKO-24h-dox


title: Shrew218Liver

source_name: Liver

value: Liver


title: 293T empty vector control replicate A FLAG immunoprecipitation

source_name: 293T cell line

value: A

value: IP


title: Shrew217Liver


title: Cth-infected YL-11

description: Cth-infected


title: Shrew218Brain

source_name: Brain

value: Brain


title: HCT116 empty vector control replicate B input

value: Input


title: Cth-infected YL-10

description: Cth-infected


title: HCT116 empty vector control replicate A FLAG immunoprecipitation


title: F1_IP


title: Shrew217Kidney

value: Kidney


title: HCT116 empty vector control replicate A input


title: F3_input

value: adult


title: WT replicate 3 total

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Reads were mapped to the human reference genome (GRCh38) using STAR v2.7.1a
Annotation of transcripts was based on GENCODE v30
The number of reads for each transcript was calculated using featureCounts
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated to represent the normalized read counts for each gene using an in-house script. Only transcripts with a FPKM greater than 1 in total RNA, nuclear RNA, and cytoplasmic RNA were included in the analysis
Genome_build: hg38

growth_protocol: Cell lines were obtained from ATCC. HCT116 cells (male) were cultured in McCoy’s 5A media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Gibco, Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco)

extract_protocol:
RNA from fractionated samples was isolated with the miRNeasy kit (Qiagen)
Whole transcriptome RNA-seq libraries from 1 µg of DNase I-treated RNA from each sample were prepared with the TruSeq Stranded Total RNA LT sample preparation kit (Illumina)

tag: fractionation

value: total RNA


title: F2_input


title: Shrew217Heart


title: Cth-infected YL-8

description: Cth-infected


title: WT-Infected YL-7

description: WT-Infected


title: Shrew217Brain


title: F2_IP

value: No.202003, Synaptic Systems, Germany


title: WT replicate 3 nuclear fraction

value: nuclear RNA fraction


title: WT-Infected YL-6

description: WT-Infected

value: Yes


title: NMR9_2Liver

organism: Heterocephalus glaber


title: NMR9_1Liver


title: WT replicate 3 cytosolic fraction

value: cytosolic RNA fraction


title: WT replicate 2 total


title: WT-Infected YL-4

description: WT-Infected


title: Sheep granulosa cells high glucose treatment group, HIGH_2

city: Baoding

first: Yong

last: Wang

address: lekai street

institute: Hebei Agricultural University

description:
G2_2
Glucose regulates germ cell proliferation and differentiation
HIGH_2

data_processing:
Tophat2（http://tophat.cbcb.umd.edu；Trapnell C et al., 2009), Hisat2（http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015), STAR（http://code.google.com/p/rna-star；Dobin A et al., 2013）
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using STAR and paired-end  clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used  the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping  result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then  FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth  and gene length for the reads count at the same time, and is currently the most  commonly used method for estimating gene expression levels.
Supplementary files format and content: count and FPKM

organism: Ovis aries

source_name: Granulosa cells

growth_protocol: the GCs were seeded in cell culture plates (Thermo Fisher Scientific, USA) at a density of 1×105/well and cultured in Dulbecco’s Modified Eagle Medium (DMEM/F12, Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA) and 1% streptomycin/penicillin mixture in a humidiﬁed atmosphere at 37 ℃ and 5% CO2 for 48 h with the medium changed every 24 h.

extract_protocol: Total RNA was extracted by Trizol method to construct a high-throughput sequencing library

treatment_protocol: The GCs were allocated to six treatments and cultured in 6-well plates at a density of 1×106/well using DMEM/F12 medium supplemented with 10% FBS. All treatments were cultured without glucose and serum but containing streptomycin/penicillin mixture (1%) for 8 h; then, the treatments received various solutions of glucose and were cultured for an additional 24 h as follows: 0 mM (i.e., zero glucose), 2.1 mM (378.3 μg/ml), 4.2 mM (756.6 μg/ml), 8.4 mM (1513.2 μg/ml), 16.8 mM (3026.4 μg/ml), 33.6 mM (6052.8 μg/ml). These doses were designed to span the normal physiological ranges of follicles

value: Granulosa cells

tag: treatment

value: Granulosa cells were cultured with glucose concentration of 33.6 mM

tag: strain

value: thin-tailed Han


title: Sheep granulosa cells high glucose treatment group, HIGH_3

description:
G2_3
Glucose regulates germ cell proliferation and differentiation
HIGH_3


title: NMR8Lung

source_name: Lung

value: Lung


title: WT replicate 2 nuclear fraction

value: WT


title: WT-Infected YL-5

description: WT-Infected


title: NMR8Kidney


title: WT-Infected YL-3

description: WT-Infected


title: WT replicate 2 cytosolic fraction


title: Cth-pool YL-2

description: Cth-pool

value: No

value: Cth-/-


title: Sheep granulosa cells low-glucose treatment group, LOW_3

description:
G1_3
Glucose regulates germ cell proliferation and differentiation
LOW_3

value: Granulosa cells were cultured with glucose concentration of 8.4 mM


title: NMR8Brain

value: Brain


title: WT replicate 1 total


title: WT-pool YL-1

description: WT-pool


title: Sheep granulosa cells low-glucose treatment group, LOW_2

description:
G1_2
Glucose regulates germ cell proliferation and differentiation
LOW_2


title: NMR6Lung


title: NMR6Kidney


title: F1_input

value: female


title: WT replicate 1 nuclear fraction


title: WT replicate 1 cytosolic fraction


title: Sheep granulosa cells low-glucose treatment group, LOW_1

description:
G1_1
Glucose regulates germ cell proliferation and differentiation
LOW_1


title: Sheep granulosa cells blank control group, CON_3

description:
CK_3
Glucose regulates germ cell proliferation and differentiation
CON_3

value: Granulosa cells were cultured with 0mM glucose


title: NMR6Heart

value: Heart


title: NMr6Brain


title: NMR4Skin

value: Skin


title: RBM33 KO clone2 replicate 2 nuclear fraction

value: RBM33 KO clone2


title: Sheep granulosa cells blank control group, CON_2

description:
CK_2
Glucose regulates germ cell proliferation and differentiation
CON_2


title: Sheep granulosa cells high glucose treatment group, HIGH_1

description:
G2_1
Glucose regulates germ cell proliferation and differentiation
HIGH_1


title: Star_noseSkin

organism: Condylura cristata


title: RBM33 KO clone2 replicate 2 cytosolic fraction


title: RBM33 KO clone2 replicate 1 total

value: total RNA


title: Star_noseLung


title: Cth-infected YL-9

description: Cth-infected

value: Yes


title: RBM33 KO clone2 replicate 1 nuclear fraction

value: nuclear RNA fraction


title: NMR4Heart


title: RBM33 KO clone2 replicate 2 total


title: Star_noseLiver

value: Liver


title: Star_noseKidney

value: Kidney


title: NMR3Kidney


title: RBM33 KO clone2 replicate 1 cytosolic fraction

value: cytosolic RNA fraction


title: RBM33 KO clone1 replicate 2 total

value: RBM33 KO clone1


title: TEC, CD31-positive cells from glioblastoma on Matrigel, patient3

type: RNA

city: Cleveland

first: Candece

middle: L

last: Gladson

state: OH

address: 9500 Euclid Ave.

department: Cancer Biology

institute: Cleveland Clinic

hyb_protocol: GeneChipTM Expression Wash, Stain and Scan for Expression Cartridge Arrays, Perfomed in Gene Expression & Genotyping Facility of Case Western Reserve University

data_processing: Data were processed using EASE software. Gene expression level is presented in Log2 scale after normalization by the Robust Multichip Analysis (RMA).

label: Biotin

source_name: CD31-positive cells from glioblastoma, ccf2390 from the Cleveland Clinic Brain Tumor Bank

label_protocol: GeneChip® 3' IVT Express Kit, Perfomed in Gene Expression & Genotyping Facility of Case Western Reserve University

growth_protocol: Cells were incubated on Matrigel until similar densities of tubes were formed.

extract_protocol: Cells were retrieved using Cell Recovery Solution (BD Biosciences, 354253) when similar densities of tubes were formed on Matrigel, and total RNA was extracted using RNeasy mini kit (Qiagen, 74104).

value: CD31-positive cells

tag: disease state

value: glioblastoma

tag: growth

value: cultured on Matrigel


title: NMR4Liver


title: TEC, CD31-positive cells from glioblastoma on Matrigel, patient2

scan_protocol: GeneChipTM Expression Wash, Stain and Scan for Expression Cartridge Arrays, Perfomed in Gene Expression & Genotyping Facility of Case Western Reserve University

source_name: CD31-positive cells from glioblastoma, ccf2352 from the Cleveland Clinic Brain Tumor Bank


title: NEC, normal brain endothelial cells on Matrigel, person3

source_name: normal primary human brain microvascular endothelial cells, ACBRI 623 from Cell Systems

value: normal


title: TEC, CD31-positive cells from glioblastoma on Matrigel, patient1

source_name: CD31-positive cells from glioblastoma, cw880 from the Brain Tumor Bank of the University Hospitals


title: Sheep granulosa cells blank control group, CON_1

description:
CK_1
Glucose regulates germ cell proliferation and differentiation
CON_1

value: Granulosa cells

value: thin-tailed Han


title: Star_noseHeart


title: NEC, normal brain endothelial cells on Matrigel, person2

source_name: normal primary human brain microvascular endothelial cells, ACBRI 422 from Cell Systems


title: NMR3Brain

value: Brain


title: NMR33Skin


title: NEC, normal brain endothelial cells on Matrigel, person1

source_name: normal primary human brain microvascular endothelial cells, ACBRI 376 from Cell Systems


title: RBM33 KO clone1 replicate 2 cytosolic fraction

source_name: HCT116 colon cancer cell line


title: TEC, CD31-positive cells from glioblastoma as Monoalyer on gelatin, patient4

growth_protocol: Cells were incubated in monolayer until total RNAs were isolated.

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen, 74104).

value: cultured as monolayer on gelatin


title: TEC, CD31-positive cells from glioblastoma as Monolayer on gelatin, patient2


title: TEC, CD31-positive cells from glioblastoma as Monolayer on gelatin, patient5

source_name: CD31-positive cells from glioblastoma, ccf2388 from the Cleveland Clinic Brain Tumor Bank


title: RBM33 KO clone1 replicate 1 total


title: NMR33Lung

value: Lung


title: N2Skin

organism: Myocastor coypus

value: Skin


title: N1Skin


title: TEC, CD31-positive cells from glioblastoma as Monolayer on gelatin, patient6


title: RBM33 KO clone1 replicate 2 nuclear fraction


title: NMR16Skin


title: TEC, CD31-positive cells from glioblastoma as Monolayer on gelatin, patient3

source_name: CD31-positive cells from glioblastoma, ccf2277 from the Cleveland Clinic Brain Tumor Bank


title: NEC, normal brain endothelial cells as Monolayer on gelatin, person2

value: primary human brain microvascular endothelial cells


title: N2Liver


title: N2Kidny

source_name: Kidney


title: NMR4Kidney


title: NMR17Skin


title: CRISPR screen unsorted population replicate 2

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Galaxy: Clip adapter GTTTTAGA and CGGTGTTTC
Galaxy: Collapse sequences
Galaxy: FASTA-to-tabular
MAGeCK sgRNA enrichment
Genome_build: hg38
Supplementary_files_format_and_content: Normalized read counts of sgRNAs

extract_protocol:
Genomic DNA was isolated from unsorted cells using the MasterPure Complete DNA Purification kit (Lucigen) and from sorted cells by phenol-chlorofom extraction
Sequencing libraries were generated using two sequential rounds of PCR using Herculase II Fusion DNA polymerase (Agilent). In the first round of PCR, 6.6 µg of genomic DNA from unsorted cells was used in each of forty 100 µl reactions, and all recovered genomic DNA from sorted cells was split into two 100 µl reactions. Following 18 cycles of PCR1 amplification, 5 µl from the pooled reaction product was used in the second round of PCR (13 – 14 cycles), using primers containing barcodes and Illumina sequencing adaptors
OTHER: CRISPR screen custom DNA library

treatment_protocol: Transduced cells were selected with 1 µg/mL puromycin (Thermo Fisher Scientific)

value: NORAD-IRES-GFP reporter cell line clone 2


title: Star_noseBrain


title: NMR33Liver


title: NMR33Heart

source_name: Heart

value: Heart


title: N2Heart


title: CRISPR screen unsorted population replicate 1

value: NORAD-IRES-GFP reporter cell line clone 1


title: NMR16Heart


title: CRISPR screen dim-sorted population replicate 1


title: NMR15Heart


title: RBM33 KO clone1 replicate 1 nuclear fraction

value: nuclear RNA fraction


title: RBM33 KO clone1 replicate 1 cytosolic fraction

value: cytosolic RNA fraction


title: N2Lung


title: NMR33Brain


title: N1Lung


title: NMR16Kidney

value: Kidney


title: NMr15Brain


title: NEC, normal brain endothelial cells as Monolayer on gelatin, person3


title: CRISPR screen dim-sorted population replicate 2


title: N1Kidney


title: NC5_40_n1

city: Montréal

first: Gabrielle

last: Deschamps-Francoeur

address: 110 Avenue des Pins, Ouest

country: Canada

institute: Institut de Recherches Cliniques de Montréal

description: Negative control

data_processing:
The base calls were converted to fastq files using bcl2fastq v2.20 (Illumina) with the following options: --minimum-trimmed-read-length 13, --mask-short-adapter-reads 13, --no-lane-splitting.
Fastq files were checked for quality using FastQC v0.11.15 and trimmed using Trimmomatic v0.36 with TRAILING:30 to remove Illumina sequencing adapters and portions of reads of low quality, respectively. Reads were aligned using STAR v 2.6.1a with the following options:  --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5 ConcordantPair. Only primary alignments were kept using samtools view -F 256 (v1.5).
The gene quantification was done using CoCo correct_count module (v.0.2.5p1) with the option -s 2 and -p.
DESeq2 was used for differential expression analysis using raw counts obtained by CoCo.
The alternative splicing analysis was done using MAJIQ v2.2 and VOILA with the option --threshold 0.1.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocellular carcinoma

growth_protocol: HepG2 cells were cultured in complete Eagle’s Minimum Essential Medium (EMEM from Wisent) and passaged twice a week,according to ATCC guidelines.

extract_protocol:
Total RNA extraction from transfected HepG2 cells was performed using RNeasy mini kit (Qiagen) as recommended by the manufacturer including on column DNase digestion with RNase-Free DNase Set (Qiagen). However, 1.5 volumes Ethanol 100% was used instead of the recommended 1 volume ethanol 70% in order to retain smaller RNA. RNA integrity of each sample was assessed with an Agilent 2100 Bioanalyzer. RNA was reversed transcribed using Transcriptor reverse transcriptase (Roche) and knockdown levels were evaluated by qPCR.
RNAseq librairies were generated from 1ug DNA-free total RNA/condition using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760S) and following the Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) . The resulting ibrairies were submitted to a total of 10 cycles of amplification then purified using 0.9X Ampure XP beads. Quality and size was assessed with an Agilent 2100 Bioanalyser. Librairies were then quantified using a Qubit fluorometer, pooled at equimolar concentration and 1.8pM was sequenced on Illumina’s NextSeq 500 using a NextSeq 500/550 High Output Kit v2.5 (150 cycles) paired-end 2x75bp.

treatment_protocol: Trypsinized cells were then seeded at 350000 cells/well in 6 well plates in 1ml EMEM. Cells were transfected 24 hours later with 2 different ASOs targeting SNORD126 (30nM or 40nM) using Lipofectamine 2000 (LIFE technologies) and optiMEM (Wisent). A scrambled ASO was used as a negative control. Cells were harvested 48 hours post transfection, washed and pelleted, then resuspended in 1ml Trizol and stored at -80℃ until RNA extraction. This was repeated 3 times to obtain biological triplicates.


title: NC5_40_n2

description: Negative control


title: N1Heart


title: NEC, normal brain endothelial cells as Monolayer on gelatin, person1


title: N1Liver

source_name: Liver

value: Liver


title: NMR11Liver


title: TEC, CD31-positive cells from glioblastoma as Monolayer on gelatin, patient1

source_name: CD31-positive cells from glioblastoma, cw850 from the Brain Tumor Bank of the University Hospitals

value: CD31-positive cells

value: glioblastoma


title: EMR2Skin

organism: Scalopus aquaticus

source_name: Skin


title: H358

city: Sevilla

first: Amancio

last: Carnero

state: Sevilla

address: Maura Montaner sn

department: Oncohematology and Genetics

country: Spain

institute: IBIS/CSIC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Celfiles were read and processed using R/Bioconductor 3.6.3. Raw expression data was normalized following the RMA method (Robust Multi-array Average) with default options from the affy package (version 1.64.0) in R. Expression was summarized at probeset level.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol according to manufacturer instructions

tag: cell line

value: NSCLC


title: EMR2Liver


title: NC5_30_n1

description: Negative control


title: NC5_30_n0

description: Negative control


title: K8Skin

organism: Ondatra zibethicus


title: HC827


title: H520


title: SNORD126_ASO2_40_n2

description: SNORD126 knockdown


title: K8Lung


title: EMR2Kidney


title: K8Liver


title: H3122


title: EMR2Heart


title: H226


title: H2228


title: H460


title: K8Kidney


title: EMR2Brain

source_name: Brain


title: SNORD126_ASO2_30_n1

description: SNORD126 knockdown


title: EMR1Skin


title: SNORD126_ASO2_40_n1

description: SNORD126 knockdown


title: SNORD126_ASO2_30_n0

description: SNORD126 knockdown


title: EMR1Liver


title: EMR1Kidney


title: H2009


title: SNORD126_ASO1_40_n1

description: SNORD126 knockdown


title: K7Lung

source_name: Lung


title: K7Skin


title: SNORD126_ASO1_40_n2

description: SNORD126 knockdown


title: K7Liver


title: H1975


title: SNORD126_ASO1_30_n1

description: SNORD126 knockdown


title: K7Kidney


title: H1781


title: H1437


title: H1650


title: K8Heart


title: T4563

city: Taipei

first: Kuo-Sheng

last: Wu

address: No.250, Wuxing St., Xinyi Dist.

country: Taiwan

institute: Taipei Medical University

data_processing:
kallisto 0.46 program used for basecalling.
Import transcript abundance estimatese by tximport 1.14.0.
Count data transformated by DESeq2 1.26.0 with variance stabilizing transformations (VST) method.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include transformed values for each Sample.

source_name: medulloblastoma tumor tissue

extract_protocol:
50 ug tumor tissue was harvested using Trizol reagent, and extracted RNA. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#FC-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: subgroup

tag: gender

value: M


title: SNORD126_ASO1_30_n0

description: SNORD126 knockdown


title: EMR1Brain

value: Brain


title: CHHLiver5

organism: Cricetulus barabensis


title: RNA-seq-ESC-2i-24h-dox_Rep2

data_processing:
Quality filtering using Trimmomatic
alignment using STAR
Read counting in genes using HT-seq count
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Table of normalized (read per million) reads for the three different batches

source_name: mouse embryonic pluripotent stem cells culture in 2i medium where forced expression of Mesp1 is dox-inducible

treatment_protocol: Doxycyclin was added to induce the expression of Mesp1

value: WT

tag: differentiation time

value: dox

value: embryonic pluripotent stem cells


title: Calu3


title: K3Skin

value: Skin


title: CHH5Heart


title: RNA-seq-ESC-2i-24h-dox_Rep1

tag: condition


title: Calu1

tag: cell type


title: RNA-seq-ESC-2i-24h-nodox_Rep2


title: CHH5Brain

tag: tissue


title: K7Heart


title: T4784


title: K3Lung

value: Lung


title: RNA-seq-ESC-2i-24h-nodox_Rep1


title: TM241


title: K3Liver


title: K3Kidney


title: CHH4Kidney


title: TM205

value: F


title: CHH5Kidney


title: T4593


title: RNA-seq_batch1_WT_24h_dox_rep1

source_name: Differentiating mouse embryonic pluripotent stem cells where forced expression of Mesp1 is dox-inducible

tag: time


title: EMR1Heart

value: Heart


title: T1771


title: K2Skin


title: T4682


title: T4656


title: K2Liver


title: A549


title: CHH3Kidney


title: CHH3Brain


title: CH120


title: T2023

value: SHH


title: RNA-seq_batch1_WT_24h_no_dox_rep1


title: RNA-seq_batch1_WT_12h_dox_rep2


title: K2Lung


title: RNA-seq_batch1_WT_24h_dox_rep2


title: K3Heart


title: K2Kidney


title: T2260


title: RNA-seq_batch1_WT_24h_no_dox_rep2


title: CHH4Brain


title: RNA-seq_batch1_WT_12h_no_dox_rep2


title: CHH3Heart


title: RNA-seq_batch1_WT_12h_dox_rep1


title: T216


title: CHH2Skin


title: K1Lung


title: T73


title: CHH2Lung


title: RNA-seq_batch1_WT_12h_no_dox_rep1


title: CHH4Heart


title: K1Liver


title: K1Kidney


title: CHH2Kidney


title: CHH2Heart


title: RNA-seq_batch1_WT_0h_no_dox_rep2


title: RNA-seq_batch1_WT_0h_no_dox_rep1


title: K2Heart


title: T15


title: T3272


title: ATAC-seq-WT-24h-dox-rep2


title: T4737


title: CHH1Lung


title: ATAC-seq-WT-24h-no-dox-rep2


title: CHH2Brain


title: TM170


title: CHH1Kidney


title: T4619

value: WNT


title: ATAC-seq-WT-12h-dox-rep2


title: Ellobius3Skin

organism: Bramus lutescens


title: Ellobius3Liver


title: CHH1Brain


title: BTR3Lung

organism: Neotoma cinerea


title: TM111

source_name: TM111: MB tumor tissue

tag: tissue source

value: patient

tag: suptype

value: childhood medulloblastoma (MB) tumor


title: T4346

source_name: T4346: MB tumor tissue


title: Ellobius3Lung


title: CHH1Heart


title: T1882

source_name: T1882: MB tumor tissue


title: Ellobius3Heart


title: K1Heart


title: Ellobius3Brain


title: ATAC-seq-WT-12h-no-dox-rep2

tag: genotype


title: Ellobius3Kidney

value: Kidney


title: 203845

type: genomic

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

source_name: pancreatic acinar cell carcinoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

value: pancreatic acinar cell carcinoma


title: BTR3Kidney


title: Ellobius2Skin


title: T2044

source_name: T2044: MB tumor tissue


title: PKD/Mhm (Cy/+) [PKD_23]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: rn6
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

organism: Rattus norvegicus

extract_protocol:
Left kidney was removed and snap frozen in liquid nitrogen. RNA was isolated with Rneasy mini kit Qiagen
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Stem cells injection (i.p. or i.v.) once per month for 6 months

value: Control

value: PKD/Mhm (Cy/+)

tag: age

value: 8 months


title: T4046

source_name: T4046: MB tumor tissue


title: ATAC-seq-WT-0h-no-dox-rep2


title: T4325

source_name: T4325: MB tumor tissue


title: Ellobius2Lung


title: BTR3Liver

value: Liver


title: PKD/Mhm (Cy/+) [PKD_24]

source_name: Kidney


title: PKD/Mhm (Cy/+) [PKD_22]


title: BTR3Heart

source_name: Heart


title: PKD/Mhm (Cy/+) + CM [PKD_21]

value: CM


title: BTR2Liver

source_name: Liver


title: BTR2Lung


title: Ellobius2Liver


title: BTR2Kidney


title: PKD/Mhm (Cy/+) + CM [PKD_19]


title: CH89

source_name: CH89: MB tumor tissue


title: T1444

source_name: T1444: MB tumor tissue


title: Ellobius2Heart


title: BTR2Heart


title: T4042

source_name: T4042: MB tumor tissue


title: RT742

source_name: RT742: MB tumor tissue


title: PKD/Mhm (Cy/+) [PKD_18]


title: Ellobius2Brain

source_name: Brain

value: Brain


title: PKD/Mhm (Cy/+) + i.p. ASC [PKD_17]


title: PKD/Mhm (Cy/+) + i.p. ASC [PKD_16]


title: Ellobius1Skin

source_name: Skin


title: Ellobius2Kidney


title: Ellobius1Lung

source_name: Lung


title: T4060

source_name: T4060: MB tumor tissue


title: BTR1Live1


title: PKD/Mhm (Cy/+) + i.p. ASC [PKD_15]


title: TM52

source_name: TM52: MB tumor tissue


title: PKD/Mhm (Cy/+) + i.v. ASC [PKD_14]


title: BTR1Heart


title: RT841

source_name: RT841: MB tumor tissue


title: GH9Heart

organism: Mesocricetus auratus


title: Ellobius1Liver


title: Ellobius1Kidney


title: PKD/Mhm (Cy/+) + i.v. ASC [PKD_13]


title: GH9Brain


title: T2056

source_name: T2056: MB tumor tissue


title: Ellobius1Heart


title: GH8Heart


title: PKD/Mhm (Cy/+) [PKD_12]


title: T3698

source_name: T3698: MB tumor tissue


title: PKD/Mhm (Cy/+) + CM [PKD_11]


title: GH8Brain


title: Ellobius1Brain


title: Chin4Skin

organism: Chinchilla lanigera


title: BTR1Kidney


title: PKD/Mhm (Cy/+) + i.v. ASC [PKD_10]


title: GH7Liver


title: GH7Brain


title: T1095

source_name: T1095: MB tumor tissue


title: Chin4Liver


title: T1307

source_name: T1307: MB tumor tissue


title: PKD/Mhm (Cy/+) + i.v. ASC [PKD_8]

source_name: Kidney


title: T4201

source_name: T4201: MB tumor tissue


title: Chin4Lung


title: T1090

source_name: T1090: MB tumor tissue


title: GH6Heart

source_name: Heart


title: T3635

source_name: T3635: MB tumor tissue


title: Chin4Heart


title: RT1294

source_name: RT1294: MB tumor tissue


title: GH5Kidney


title: GH6Brain


title: PKD/Mhm (Cy/+) + i.p. ASC [PKD_6]


title: T3654

source_name: T3654: MB tumor tissue


title: PKD/Mhm (Cy/+) + i.p. ASC [PKD_5]


title: PKD/Mhm (Cy/+) + i.v. ASC [PKD_9]


title: GH4Skin


title: GH5Heart


title: Chin4Brain

source_name: Brain


title: T1686

source_name: T1686: MB tumor tissue


title: Chin4Kidney


title: Chin3Skin

source_name: Skin


title: Chin3Lung

source_name: Lung


title: GH4Lung


title: PKD/Mhm (Cy/+) + i.p. ASC [PKD_7]


title: PKD/Mhm (Cy/+) [PKD_1]


title: Chin3Liver

source_name: Liver


title: Chin3Kidney


title: PKD/Mhm (Cy/+) + CM [PKD_2]


title: GH4Liver


title: CH1

source_name: CH1: MB tumor tissue


title: T1180

source_name: T1180: MB tumor tissue


title: Chin3Heart


title: GH4Kidney


title: T1015

source_name: T1015: MB tumor tissue


title: GH3Skin


title: Chin3Brain


title: T2792

source_name: T2792: MB tumor tissue


title: GH3Lung


title: Chin2Skin


title: PKD/Mhm (Cy/+) + i.v. ABCB5+ [ivABCB5_43]


title: PKD/Mhm (Cy/+) + i.v. ABCB5+ [ivABCB5_37]


title: PKD/Mhm (Cy/+) + i.v. ABCB5+ [ivABCB5_36]


title: T1080

source_name: T1080: MB tumor tissue


title: GH3Liver


title: PKD/Mhm (Cy/+) + i.v. ABCB5+ [ivABCB5_42]

source_name: Kidney


title: Chin2Kidney


title: GH3Kidney


title: Chin1Lung


title: TM28

source_name: TM28: MB tumor tissue


title: GH3Heart


title: PKD/Mhm (Cy/+) + i.p. ABCB5+ [ipABCB5_41]


title: PKD/Mhm (Cy/+) + i.v. ABCB5+ [ivABCB5_28]


title: Chin1Liver


title: T1184

source_name: T1184: MB tumor tissue


title: GH2Lung


title: Chin2Brain


title: CH127

source_name: CH127: MB tumor tissue


title: GH2Liver


title: PKD/Mhm (Cy/+) + i.p. ABCB5+ [ipABCB5_38]


title: Chin1Kidney


title: T4247

source_name: T4247: MB tumor tissue


title: T1950

source_name: T1950: MB tumor tissue


title: Cap9Skin

organism: Hydrochoerus hydrochaeris


title: PKD/Mhm (Cy/+) + i.p. ABCB5+ [ipABCB5_31]


title: PKD/Mhm (Cy/+) + i.p. ABCB5+ [ipABCB5_32]


title: PKD/Mhm (Cy/+) + i.v. ASC [PKD_3]


title: GH1Skin


title: T66

organism: Homo sapiens

source_name: T66: MB tumor tissue


title: PKD/Mhm (Cy/+) + i.v. ABCB5+ [ivABCB5_33]


title: Chin1Heart

source_name: Heart


title: T208

source_name: T208: MB tumor tissue


title: PKD/Mhm (Cy/+) + i.p. ABCB5+ [ipABCB5_29]


title: GH1Lung


title: T113

source_name: T113: MB tumor tissue


title: T709

source_name: T709: MB tumor tissue


title: PKD/Mhm (Cy/+) [Ctrl_24]

value: Ctrl


title: GH1Kidney


title: PKD/Mhm (Cy/+) + i.p. ABCB5+ [ipABCB5_30]


title: GH1Liver

source_name: Liver


title: GH10Skin

source_name: Skin

value: Skin


title: T579

source_name: T579: MB tumor tissue


title: RT1335

source_name: RT1335: MB tumor tissue


title: Cap9Brain

source_name: Brain


title: GH10Brain


title: Cap8Lung

source_name: Lung

value: Lung


title: PKD/Mhm (Cy/+) [Ctrl_23]

source_name: Kidney


title: PKD/Mhm (Cy/+) [Ctrl_22]


title: T4436

source_name: T4436: MB tumor tissue


title: GH2Kidney


title: Cap8Kidney


title: Cap8Liver


title: Cap9Liver


title: PKD/Mhm (Cy/+) [Ctrl_18]


title: Cap9Lung


title: Cap8Brain


title: T3256

source_name: T3256: MB tumor tissue


title: PKD/Mhm (Cy/+) [Ctrl_1]


title: PKD/Mhm (Cy/+) [Ctrl_12]


title: PKD/Mhm (Cy/+) + CoCM [CoCM_40]

value: CoCM


title: Cap7Kidney


title: PKD/Mhm (Cy/+) + CoCM [CoCM_35]


title: Cap7Liver


title: T692

source_name: T692: MB tumor tissue


title: Cap7Heart

value: Heart


title: T4053

source_name: T4053: MB tumor tissue


title: PKD/Mhm (Cy/+) + CoCM [CoCM_39]


title: T1425

source_name: T1425: MB tumor tissue

value: SHH


title: T4394

source_name: T4394: MB tumor tissue

value: WNT


title: T739

source_name: T739: MB tumor tissue

value: patient


title: CH53

source_name: CH53: MB tumor tissue

value: childhood medulloblastoma (MB) tumor


title: TM4

source_name: TM4: MB tumor tissue


title: Cap7Brain


title: PKD/Mhm (Cy/+) + CoCM [CoCM_27]


title: Cap7Skin


title: Cap6Skin


title: PKD/Mhm (Cy/+) + CoCM [CoCM_26]


title: BEAS-2B-arsenic plus BaP-exposed_3

city: Lexington

first: Zhishan

state: Kentucky

address: Toxicology, 256 HSRB, 1095 Veterans Drive

department: Toxicology and Cancer Biology

institute: University Of Kentucky

hyb_protocol: All labeling, hybridization and scanning steps were carried out by ArrayStar, Inc. Rockville, MD.

data_processing: Raw signal intensities were normalized by quantile normalization method in GeneSpring GX v12.1. Low intensity mRNAs were filtered. mRNAs that at least 3 out of 12 samples have flags in Present or Marginal were chosen for further analysis.

source_name: BEAS-2B-arsenic plus BaP-exposed

growth_protocol: All BEAS-2B cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) supplemented with 5% fetal bovine serum (FBS, Sigma), 1% penicillin/streptomycin (10,000 U/mL, Gibico)

extract_protocol: Total RNA samples were isolated from the passage-matched BEAS-2B-Control, BEAS-2B-As, BEAS-2B-BaP, and BEAS-2B-As+BaP cells using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol.

treatment_protocol: BEAS-2B cells were continuously exposed to a vehicle control (DMSO), arsenic (NaAsO2, 1 μM) or BaP (2.5 μM) alone, or arsenic plus BaP (1 μM of NaAsO2 + 2.5 μM of BaP) for 30 weeks.

value: bronchial epithelial cell


title: T4186

source_name: T4186: MB tumor tissue


title: BEAS-2B-arsenic plus BaP-exposed_2

scan_protocol: All labeling, hybridization and scanning steps were carried out by ArrayStar, Inc. Rockville, MD.


title: PKD/Mhm (Cy/+) + CoCM [CoCM_34]


title: RT593

source_name: RT593: MB tumor tissue


title: Cap6Kidney

value: Kidney


title: HCC_122_T

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools). Gene expression quantification were obtained using HTSeq-count with Gencode v7. RSEM quantification at gene level was produced with NCBI Refseq (2011).
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  For HTSeq, the first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count. For RSEM, the results are combined to three output files: expected read counts, RPKM and TPM value for each gene for all 20 samples in each column.

source_name: normal liver tissue adjacent to tumor

extract_protocol:
Total RNA was isolated from the tissues using RNA Mini Spin Column of Enzy Max LLC (Lexington, KY) according to the manufacturer’s instructions. DNase (Thermo Scientific, Rockford, IL, Cat.# EN0521) was added to the first wash solution at 10µg/70µl and incubated for 15 min at room temperature to remove genomic DNA contamination
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

value: normal liver

value: male


title: HCC_122_N

source_name: liver tumor

value: Hepatocellular carcinoma


title: T4356

source_name: T4356: MB tumor tissue


title: Cap6Heart

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression

source_name: Heart

extract_protocol:
Tissues were extracted from recently (<12hr) deceased or euthanized animals and flash frozen in liquid nitrogen. Animals not euthanized in lab were kept at 4°C and processed within 12hr of death. Frozen tissues were pulverized using a Cell Crusher piston chilled with liquid nitrogen to produce uniform powdered tissue. Approximately 30mg of frozen tissue powder was used for Trizol RNA extraction. Contaminating DNA was removed from RNA samples using Purelink DNase kit along with Purelink RNA columns. Purified RNA quality was checked using agarose gel examination for rRNA integrity and Qubit analysis
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
Ribo-depletion for RNAseq


title: HCC_77_T


title: BEAS-2B-arsenic plus BaP-exposed_1

label_protocol: All labeling, hybridization and scanning steps were carried out by ArrayStar, Inc. Rockville, MD.


title: CH107

source_name: CH107: MB tumor tissue


title: BEAS-2B-BaP-exposed_3


title: BEAS-2B-BaP-exposed_2


title: Cap6Brain

source_name: Brain


title: BEAS-2B-arsenic-exposed_1


title: BEAS-2B-BaP-exposed_1


title: HCC_77_N


title: Cap6Liver

source_name: Liver

value: Liver


title: BEAS-2B-arsenic-exposed_2


title: BEAS-2B-arsenic-exposed_3


title: BEAS-2B-Vehicle Control-exposed_2

source_name: BEAS-2B-Vehicle Control-exposed


title: BEAS-2B-Vehicle Control-exposed_3


title: BEAS-2B-Vehicle Control-exposed_1


title: CD73ko_MCAO_3

status: Public on May 17 2022

city: Hamburg

first: Björn

last: Rissiek

state: Hamburg

address: Martinistraße 52

department: Department of Neurology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: 50 ng of whole brain mRNA from sham surgery CD73fl/fl mice, stroked CD73fl/fl mice and stroked CD73–/– mice (n = 4 / group) were hybridized to the cartridge and the chip was run on a nCounter SPRINT profiler

scan_protocol: NanoString Technologies protocol

data_processing: NanoString Technologies nSolver Advanced Software protocol (Default settings)

organism: Mus musculus

source_name: whole brain

extract_protocol: Brains were homogenized in 1 ml TRIzol reagent per 50-100 mg tissue (Ambion).

treatment_protocol: CD73ko and control mice were subjected to 50min of transient middle cerebral artery occlusion or sham surgery. Three days after the treament mice were sacrificed and brains were extracted.

tag: Sex

tag: group

value: CD73ko mice that underwent tMCAO surgery


title: control_MCAO_2

tag: strain

value: CD73floxed that underwent tMCAO surgery


title: conv. PTX rep1 [DK21014_07]

city: Tokyo

first: Nozomu

last: Yanaihara

address: 3-25-8, Nishi-shinbashi, Minato-ku

country: Japan

institute: The Jikei Univ.

data_processing:
Libraries were sequenced using single-end 75 bp on a NextSeq500 instrument to an average depth of 2.8 M clusters per sample.
All data analyses were carried out using Strand NGS 3.4.
In addition to trimming of adapters and poly-A from fastq files, all read sequences were trimmed by 6 bp from the 5′ end following the manufacturer's recommendations.
Assembly: Reads were mapped to the human genome hg19.
Supplementary files format and content: DESeq normalization

source_name: Ovary

extract_protocol:
We used the manual method using TRIzol reagent according to the manufacturer’s instruction for total RNA extraction.
Purified 500ng of total RNA was used for RNA library preparation according to the instructions of the Quant Seq 3’ mRNA-seq library preparation kit FWD for Illumina.

value: Ovary

value: OVISE

value: Ovarian cancer

value: WT

tag: treatment

value: conv. PTX+gamma irradation


title: control_sham_3

value: shamed CD73flox


title: control_sham_2


title: PBS rep2 [DK21014_02]

value: PBS+gamma irradation


title: conv. PTX rep2 [DK21014_08]


title: CD73ko_MCAO_2


title: dd PTX rep2 [DK21014_11]

value: dd PTX+gamma irradation


title: CD73ko_MCAO_1


title: control_sham_4


title: control_MCAO_3


title: bevacizumab rep1 [DK21014_04]

value: bevacizumab+gamma irradation


title: control_MCAO_1


title: control_sham_1


title: control_MCAO_4


title: dd PTX rep3 [DK21014_12]


title: bevacizumab rep2 [DK21014_05]


title: dd PTX rep1 [DK21014_10]


title: PBS rep1 [DK21014_01]


title: PBS rep3 [DK21014_03]


title: conv. PTX rep3 [DK21014_09]


title: CD73ko_MCAO_4


title: E_2silkForebrainday20_S7_quant

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich

data_processing:
bclfastq by Illumina (v. 2.19).
Quantification with Salmon 1.1 using Gencode version 33 as the gene model.
DESeq2 (v. 1.3).
Assembly: GRCh38
Supplementary files format and content: quant.sf files

source_name: Silk organoid culture day 20

growth_protocol: To start 3D organoid formation, homogeneous hPSC culture at 75-90% confluency of the well area was washed with DPBS (-/-), Thermo Fisher Scientific, 14200075) and incubated with Accutase solution (50 μL/cm², Thermo Fisher Scientific, A1110501) for 5 min at 37°C. The cells were then centrifuged, resuspended in mTeSR1 (Stem Cell Technologies, 05850) with 10μM Y-27632 and counted. Single cell suspension was then seeded at a density of 8000 cells/well in an ultra-low attachment 96-well plate (Costar, round bottom, REF 7007) and supplemented with mTeSR1 with 10μM Y-27632 to reach a final volume of 250 μL/well as reported in Lancaster et al[12]. After two days of culture, 50% of media was replaced with mTesR1 without the Y-27632 supplement. , Thermo Fisher Scientific, 14200075) and incubated with Accutase solution (50 μL/cm², Thermo Fisher Scientific, A1110501) for 5 min at 37°C. The cells were then centrifuged, resuspended in mTeSR1 (Stem Cell Technologies, 05850) with 10μM Y-27632 and counted. Single cell suspension was then seeded at a density of 8000 cells/well in an ultra-low attachment 96-well plate (Costar, round bottom, REF 7007) and supplemented with mTeSR1 with 10μM Y-27632 to reach a final volume of 250 μL/well as reported in Lancaster et al[12]. After two days of culture, 50% of media was replaced with mTesR1 without the Y-27632 supplement. After three additional days, differentiation medium consisting of DMEM/F12 (Thermo Fisher Scientific, 21331020), 1:100 N2 supplement (Thermo Fisher Scientific, 17502048) and 2 μg/mL Heparin (Sigma-Aldrich, H3149) was added from day 0-6 and replaced every second day. 1% minimum essential medium non-essential amino acids (MEM-NEAA; Sigma-Aldrich, M7145), 0.1% 2-mercaptoethanol (Merck, 8057400005), 1:500 penicillin-streptomycin (Thermo Fisher Scientific, 15140122), and 200 mM L-glutamine (Thermo Fisher Scientific, 25030081) were maintained for the entire differentiation period, as reported in Lancaster et al [12]. For the first 48h the medium was also supplemented with 3% Knockout Serum Replacement (KSR, Thermo Fisher Scientific, 10828010). At day 8 each organoid was transferred in a sterile dimple, embedded evenly in 30uL of matrigel (Corning, 354234) and incubated at 37°C for 25 min. After the polymerisation of matrigel was complete, the organoids were transferred in an ultra-low attachment 6 well plate (Corning, flat bottom, REF 3471) with 4mL/well of 1:1 DMEM/F12:Neurobasal medium (Thermo Fisher Scientific, 21331020 and A3582901), 1:200 N2 supplement, 1:100 B27 supplement (Thermo Fisher Scientific, 12587010) and 2.5 μg/mL insulin (Sigma-Aldrich, I9278-5ML), as reported in Lancaster et al [12]. The medium was replaced every second day. At day 15, the medium was substituted with 1:1 DMEM/F12:Neurobasal, 1:200 N2 supplement, 1:50 B27+Vitamin A supplement (Thermo Fisher Scientific, 17504044) and 2.5 μg/mL Insulin solution supplemented with 400μM Ascorbic Acid (Sigma-Aldrich, A4403-100MG). For terminal differentiation after day 25, the previously described medium was supplemented with 400μM Ascorbic Acid, 10ng/mL BDNF (Miltenyi, 130-096-286), 10ng/mL GDNF (R&D Systems, 212-GD-010) and 200μM cAMP (Sigma-Aldrich, D0627-1G).

extract_protocol:
RNeasy Micro Kit (Qiagen, 74004), in accord to manufacturer instructions.
Illumina TruSeq library preparation kit.

treatment_protocol: Silk organoids: A 20μL droplet of prepared Biosilk solution (BioLamina, BS-0101) functionalized with 5μg/mL Lam-111 (BioLamina, LN111) and 10 μM Y-27632 was placed in the centre of hydrophobic cell culture wells of a 24-well plate (Sarstedt, REF 833922500)[17]. Air bubbles were introduced into the droplets by pipetting up and down (10-15 strokes) creating a dense foam. Human pluripotent stem cells were detached using Accutase solution (50 μL/cm²) and prepared as a single cell suspension at high concentration (15’000 cells/μL in mTeSR1 with 10 μM Y-27632). A total of 75’000 cells was then added to the silk foam, dispersed homogeneously, and stabilized at 37°C for 25 min. Silk bioengineered culture was then incubated with 2mL of mTeSR1 with 10 μM Y-27632 for 5 days and then cultured following the cerebral differentiation protocol as described in Lancaster et al. [12]. Eight days after the start of differentiation, silk organoids were lift up with a scalper, detached from the bottom and grown in suspension (free floating) in a 6-well plate (Corning, 3471).

value: Forebrain organoid

tag: culture condition

value: Silk

tag: days in culture


title: A_1standardForebrainday20_S3_quant

source_name: Non-silk organoid culture day 20

value: Non-silk


title: B_2standardForebrainday20_S4_quant


title: F_3silkForebrainday20_S8_quant


title: C_3standardForebrainday20_S5_quant


title: D_1silkForebrainday20_S6_quant


title: bevacizumab rep3 [DK21014_06]

tag: cell line


title: NSH_WT-Tag-composite_INPUT

city: Memphis

first: Suzanne

middle: J

last: Baker

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

description: concatenated WF_NSH INPUTs

data_processing:
We used bbmap 38.86 bbduk and bbsplit with a hybrid mm9/dm6 genome to remove spike in fly reads from H3K4me3 ChIPseq and inputs
nf-core/chipseq V1.2.1 was used to QC, align and call peaks.
nf-core/chipseq V1.2.1 uses BWA v0.7.17-r1188, we used --keep_multi_map flag
nf-core/chipseq V1.2.1 uses MACS2 v2.2.7.1,  we used --narrow_peak and --macs_fdr 0.01 flags
nf-core/chipseq V1.2.1 uses BEDTools v2.29.2 bedGraphToBigWig to generate bigwig files
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locations of defined peaks.  bigWig files containing normalized read coverage.

source_name: Mouse e15.5 hindbrain neurosphere

extract_protocol:
Single cell suspensions were generated from cultured cells using Accutase before fixation. Samples were fixed for 5 minutes with 1% paraformaldehyde in PBS (from a frozen stock) at room temperature. Bare nuclei were suspended in shearing buffer + protease inhibitors (10 Tris HCL pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS) and sheared on a Covaris M220 ultrasonicator (Microtube, 75W, 5% duty cycle, 200 cycles per burst, 5 minutes or Millitube, 75W, 10% duty cycle, 200 cycles per burst, 15 minutes). Sonication size was verified on an Agilent Bioanalyzer using a High Sensitivity DNA Assay. For H3K4me3 ChIP-seq, sheared chromatin from drosophila melanogaster S2 cells was added to the mammalian chromatin prior to ChIP at a set ratio for each histone mark to allow for sample normalization. 400 ng of chromatin was used per ChIP reaction and for ChIP-seq, multiple ChIPs were performed and pooled as needed to generate enough chromatin for library construction. 10-20 ng of pre-IP chromatin containing spike in was kept as an input control. ChIP reactions were performed using a modified Upstate Biotechnology protocol. Briefly, sheared chromatin was diluted 1:10 with dilution buffer + protease inhibitors (21 Tris HCL pH 8.0, 1 mM EDTA pH 8.0, 167 mM NaCl, 1.1% Triton X-100, 0.1% SDS), precleared with 30 ul Fast Flow Protein A sepharose beads (GE Healthcare) and 50 μg bovine serum albumin (BSA) by rotating in a siliconized eppendorf tube at 4 C for 1-2 hours. The precleared chromatin was transferred to a tube containing the antibody of interest (see below), 30 ul Protein A sepharose beads and 50 ug BSA and rotated overnight at 4 C. The bead bound chromatin was washed once each with low salt buffer (20 mM Tris HCl pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt buffer (20 mM Tris HCl pH 8.0, 2 mM EDTA pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 1% Nonidet P-40, 1% Deoxycholate) and twice with TE (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0). The chromatin was eluted off the beads with 0.1 M NaHCO3 /1% SDS by rotating at room temperature for 30 minutes, then the supernatant was transferred to a tube with 200nM NaCl and cross links were reversed by incubating overnight at 65 C (input controls were processed along with the ChIP samples from this point on). 10ug Proteinase K was added and the tube was incubated for 2 hours at 37 C, then the DNA was cleaned up using a QiaQuick PCR Purification Kit (Qiagen) and eluted in 50 μl 10 mM Tris HCl pH 8.5. Antibodies used were (μl antibody per IP shown):  H3K4me3 (Cell Signaling 9751, lot 8; 5 μl and  FLAG (Sigma M2 #F1804, lot SLBJ4607V; 4μl).
Libraries were prepared from 5-10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation. The Ampure size selection step prior to PCR was eliminated. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer). Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems) or low pass sequencing on a MiSeq Nano v2 run (Illumina).

tag: experiment id

tag: full genotype

value: Nestin-cre; H3f3aLSL-WT-Tag/+

tag: gender

value: pooled male and female

tag: growth protocol

value: Grown under neural precursor cell conditions

tag: chip antibody

value: none (input)


title: PD2_scRNAseq_WT_Rep1

city: Seoul

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Transcripts were mapped to the mm10 reference genome using CellRanger v4.0.0 with default reference package (10X Genomics)
a
Genome_build: mm10
Supplementary_files_format_and_content: filtered feature barcode matrix files

source_name: total skin cells

extract_protocol:
Freshly dissociated unsorted skin cells from mouse skin were subjected to scRNA-seq library preparation.
For scRNA-seq, dermal and epidermal single-cell suspension were counted with hemocytometer and mixed with 1:1 ratio. Dead cells were removed using the MS columns of the Dead Cell Removal Kit (MACS) as per manufacturer’s directions. Library construction were processed according to Chromium Single Cell 3' Reagent Kits v3 Chemistry (10X Genomics) as per the manufacturer’s protocol. Library was sequenced using Illumina HiSeq X Ten platform (Illumina).

tag: agent

tag: developmental stage


title: PD4_scRNAseq_WT_Rep1


title: PD4_scRNAseq_WT_Rep2


title: TSA-PD4_scRNAseq_WT_Rep1

source_name: total skin cells after in vivo TSA treatment

value: TSA


title: TSA-PD4_scRNAseq_WT_Rep3


title: SRR5855220_wt_E12_DFL_CTCF

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

description: Reanalysis of GSM2713707

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15 (−A being used only in PE data sets).
Reads were mapped with bowtie[Langmead et al. 2012] 2.4.1 with default parameters on mm10.
Alignments with a mapping quality below 30, as well as discordant pairs for PE datasets, were discarded with samtools view version 1.8 [Li et al. 2009 and Li et al. 2011].
Coverage and peak calling were computed by macs2 [Zhang et al.2008] version 2.1.1.20160309 with options --bdg --call-summits --gsize '1870000000', and -f BAMPE for PE.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage from macs2
Supplementary_files_format_and_content: narrowPeak: peaks from macs2

source_name: distal forelimb

extract_protocol:
see original publication
see original publication

tag: tissue

value: distal forelimb

value: wild type


title: SRR5855214_wt_E12_DFL_H3K27ac

description: Reanalysis of GSM2713703

tag: genotype


title: SRR5855215_wt_E12_PFL_H3K27ac

description: Reanalysis of GSM2713704

source_name: proximal forelimb

value: proximal forelimb


title: PD2_scRNAseq_WT_Rep2


title: SRR5855221_wt_E12_PFL_CTCF

description: Reanalysis of GSM2713708


title: PD4_scRNAseq_WT_Rep3


title: PD0_scRNAseq_WT_Rep3


title: TSA-PD4_scRNAseq_WT_Rep2


title: SRR3168464_wt_E12_DFL_H3K27me3

description: Reanalysis of GSM2061125


title: PD0_scRNAseq_WT_Rep2


title: PKD1RC minus ChIP Rep 2

city: Dallas

first: Ronak

last: Lakhia

address: 5323 Harry Hines

institute: UTSW

data_processing:
The raw reads were aligned to the mouse reference genome (GRCh38/mm10) using default parameters in BWA v0.7.1230. The aligned reads were subsequently filtered for quality, and uniquely mappable reads were retained for further analysis using Samtools version 1.6 and Sambamba version 0.6.6 31,32. Library complexity was measured using BEDTools version 2.26.0 and meets ENCODE data quality standards33,34. Relaxed peaks were called using MACS version 2.1.0
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: normalized bigWig

extract_protocol:
Cells were fixed with 37% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was fragmented with micrococcal nuclease
Libraries from 5–10 ng ChIP DNA are prepared using KAPA HTP Library Preparation Kit. The ChIP DNA is quantified on the Qubit® 2.0 Fluorometer from Invitrogen Samples are end repaired, 3' ends adenylated and barcoded with mµltiplex adapters. PCR amplified libraries are purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer to ensure the library is the expected size. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using 50SR SBS v3 reagents.

tag: cell type

value: Mus musculus

value: H3K27ac (Cell Signaling 8173)


title: PKD1RC minus ChIP Rep 1


title: SRR3168462_wt_E12_PFL_H3K27me3

description: Reanalysis of GSM2061123


title: NSH_K27M-Tag-composite_INPUT

description: concatenated KF_NSH INPUTs

value: Nestin-cre; H3f3aLSL-K27M-Tag/+

value: female


title: NSH-B_K27M-Tag_FLAG_ChIP-seq

data_processing:
We used bbmap 38.86 bbduk and bbsplit with a hybrid mm9/dm6 genome to remove spike in fly reads from H3K4me3 ChIPseq and inputs
nf-core/chipseq V1.2.1 was used to QC, align and call peaks.
nf-core/chipseq V1.2.1 uses BWA v0.7.17-r1188, we used --keep_multi_map flag
nf-core/chipseq V1.2.1 uses MACS2 v2.2.7.1, we used --narrow_peak and --macs_fdr 0.01 flags
nf-core/chipseq V1.2.1 uses BEDTools v2.29.2 bedGraphToBigWig to generate bigwig files
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locations of defined peaks. bigWig files containing normalized read coverage.

growth_protocol: Grown under neural precursor cell conditions.

extract_protocol:
Single cell suspensions were generated from cultured cells using Accutase before fixation. Samples were fixed for 5 minutes with 1% paraformaldehyde in PBS (from a frozen stock) at room temperature. Bare nuclei were suspended in shearing buffer + protease inhibitors (10 Tris HCL pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS) and sheared on a Covaris M220 ultrasonicator (Microtube, 75W, 5% duty cycle, 200 cycles per burst, 5 minutes or Millitube, 75W, 10% duty cycle, 200 cycles per burst, 15 minutes). Sonication size was verified on an Agilent Bioanalyzer using a High Sensitivity DNA Assay. For H3K4me3 ChIP-seq, sheared chromatin from Drosophila melanogaster S2 cells was added to the mammalian chromatin prior to ChIP at a set ratio for each histone mark to allow for sample normalization. 400 ng of chromatin was used per ChIP reaction and for ChIP-seq, multiple ChIPs were performed and pooled as needed to generate enough chromatin for library construction. 10-20 ng of pre-IP chromatin containing spike in was kept as an input control. ChIP reactions were performed using a modified Upstate Biotechnology protocol. Briefly, sheared chromatin was diluted 1:10 with dilution buffer + protease inhibitors (21 Tris HCL pH 8.0, 1 mM EDTA pH 8.0, 167 mM NaCl, 1.1% Triton X-100, 0.1% SDS), precleared with 30 ul Fast Flow Protein A sepharose beads (GE Healthcare) and 50 μg bovine serum albumin (BSA) by rotating in a siliconized eppendorf tube at 4 C for 1-2 hours. The precleared chromatin was transferred to a tube containing the antibody of interest (see below), 30 ul Protein A sepharose beads and 50 ug BSA and rotated overnight at 4 C. The bead bound chromatin was washed once each with low salt buffer (20 mM Tris HCl pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt buffer (20 mM Tris HCl pH 8.0, 2 mM EDTA pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 1% Nonidet P-40, 1% Deoxycholate) and twice with TE (10 mM Tris HCl pH 8.0, 1 mM EDTA pH 8.0). The chromatin was eluted off the beads with 0.1 M NaHCO3 /1% SDS by rotating at room temperature for 30 minutes, then the supernatant was transferred to a tube with 200nM NaCl and cross links were reversed by incubating overnight at 65 C (input controls were processed along with the ChIP samples from this point on). 10ug Proteinase K was added and the tube was incubated for 2 hours at 37 C, then the DNA was cleaned up using a QiaQuick PCR Purification Kit (Qiagen) and eluted in 50 μl 10 mM Tris HCl pH 8.5. Antibodies used were (μl antibody per IP shown): H3K4me3 (Cell Signaling 9751, lot 8; 5 μl and FLAG (Sigma M2 #F1804, lot SLBJ4607V; 4μl).
Libraries were prepared from 5-10 ng of DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs) with the following modifications: a second 1:1 Ampure cleanup was added after adaptor ligation. The Ampure size selection step prior to PCR was eliminated. Completed libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer). Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems) or low pass sequencing on a MiSeq Nano v2 run (Illumina).

value: Neural stem cells

value: Sigma FLAG M2 #F1804 (lot SLBJ4607V)


title: NSH-D_WT-Tag_FLAG_ChIP-seq


title: NSH-F_WT-Tag_FLAG_ChIP-seq

value: male


title: NSH-E_WT-Tag_FLAG_ChIP-seq


title: NSH-C_K27M-Tag_FLAG_ChIP-seq


title: NSH-A_K27M-Tag_FLAG_ChIP-seq


title: PKD1RC minus input Rep 1

value: input


title: PD0_scRNAseq_WT_Rep1


title: PKD1RC minus input Rep 2


title: PD2_scRNAseq_WT_Rep3


title: NSH-F_WT-Tag_H3K4me3_ChIP-seq

value: Cell Signaling H3K4me3 #9751 (lot 8)


title: NSH-D_WT-Tag_H3K4me3_ChIP-seq

value: Nestin-cre; H3f3aLSL-WT-Tag/+


title: NSH-E_WT-Tag_H3K4me3_ChIP-seq


title: NSH-B_K27M-Tag_H3K4me3_ChIP-seq


title: NSH-C_K27M-Tag_H3K4me3_ChIP-seq


title: iXist-ChrX-Dom_ES_d10_Rep4

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
A11B2_ES_d1r4
iXist-ChrX-Dom_mESC_d10_AllelicRatio_table.txt

data_processing:
The standard ChrRNA-seq data mapping pipeline is reported in our previous study (Nesterova et al., 2019). Briefly, raw fastq files of read pairs were first mapped to rRNA by bowtie2 (v2.3.2; Langmead and Salzberg 2012) and rRNA-mapping reads discarded (typically <2%). The remaining unmapped reads were aligned to an N-masked mm10 genome with STAR (v2.4.2a; Dobin et al., 2013) using parameters: “-outFilterMultimapNmax 1 -outFilterMismatchNmax 4 -alignEndsType EndToEnd”.
Aligned reads were assigned to separate files for either the Cast or Dom/129S genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “- paired” parameter and a SNPfile containing the 23,005,850 SNPs between Cast and Dom/129S genomes (UCSC).
Read fragments overlapping genes, for both the ‘unsplit’ and ‘allelic’ files of each sample, were counted by the program featureCounts (Liao et al., 2014) using an annotation file of all transcripts and lncRNAs from NCBI RefSeq and the parameters “-t transcript -g gene id -s 2”.
Further allelic analysis was performed using R and RStudio on allelic count matrix output files from featureCounts. X-linked genes with at least 10 allelically-assigned fragments (i.e. containing reads that overlap SNPs) in >80% of WT samples were retained for gene silencing analysis. Gene silencing was assessed by calculating the allelic ratio of read counts, given by Xi/(Xi + Xa). An additional filter on the allelic ratio in uninduced mESCs (0.1 < allelic ratio < 0.9) was also applied, as strongly monoallelic genes are likely to be technical artifacts of singular mis-annotated SNPs.
Genome_build: mm10
Supplementary_files_format_and_content: counts tables, allelic ratio

source_name: iXist-ChrX-Dom(mESC)

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating. For NPC differentiation timepoints, mESCs were first extensively separated from feeder cells by pre-plating four times for 35-40 min each.

extract_protocol:
Between 5 x 106 (NPC) and 3 x 107 (mESC) cells were collected from confluent 90mm dishes, washed once with PBS, then snap-frozen and stored at -80oC. Chromatin extraction was performed as follows: Cell pellets were lysed on ice for 5 min in RLB (10 mM Tris pH7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40). Nuclei were then purified by centrifugation through 24% sucrose/RLB (2800 g for 10 min at 4oC), resuspended in NUN1 (20 mM Tris pH7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.1 mM DTT), and then lysed by gradual addition of an equal volume NUN2 (20 mM HEPES pH 7.9, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea, 0.1 mM DTT). After 15 min incubation on ice with occasional vortexing, the chromatin fraction was isolated as the insoluble pellet after centrifugation (2800 g for 10 min at 4oC). Chromatin pellets were resuspended in 1mL TRIzol (Invitrogen) and fully homogenenized and solubilized by eventually being passed through a 23-gauge needle 10 times . This was followed by isolation of chromatin-associated RNA through TRIzol/chloroform extraction with isopropanol precipitation. Precipitated RNA pellets were washed twice with 70% ethanol. Final ChrRNA samples were then resuspended in H2O, treated with TurboDNAse and measured by Nanodrop (both ThermoFisher). 500 ng – 1 µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit (RS-122-2301).
Illumina TruSeq stranded total RNA kit (500 ng – 1 µg of RNA)

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1μg/mL) to the culture medium and maintained for 10 days.

value: Dom/129S x Cast

value: mESC

tag: Sex

value: Female

tag: cell engineering

value: Endogenous Xist promoter replaced with TetOn Promoter (Dom/129S allele)

tag: xist (dox) induction time

value: 10 days


title: iXist-ChrX-Dom_ES_0h_mRNA_Rep1

data_processing:
Raw fastq files of read pairs were first mapped to rRNA by bowtie2 (v2.3.2; Langmead and Salzberg 2012) and rRNA-mapping reads discarded (typically <2%). The remaining unmapped reads were aligned to an N-masked mm10 genome with STAR (v2.4.2a; Dobin et al., 2013) using parameters: “-outFilterMultimapNmax 1 -outFilterMismatchNmax 4 -alignEndsType EndToEnd”.
Aligned reads were assigned to separate files for either the Cast or Dom/Dom/129S genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “- paired” parameter and a SNPfile containing the 23,005,850 SNPs between Cast and Dom/Dom/129S genomes (UCSC).
Read fragments overlapping genes, for both the ‘unsplit’ and ‘allelic’ files of each sample, were counted by the program featureCounts (Liao et al., 2014) using an annotation file of all transcripts and lncRNAs from NCBI RefSeq and the parameters “-t transcript -g gene id -s 2”.
Transcripts per kilobase Million (TPM) transformation was performed on counts matrix. This involves a step of calculating gene length (in bp). As mRNA-seq data contains very few intronic reads, exonic sequence lengths for each gene were used.
Genome_build: mm10
Supplementary_files_format_and_content: counts table

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating.

extract_protocol:
The Dynabeads® mRNA DIRECT™ Kit  was used for the isolation of pure mRNA directly from crude samples  (Invitrogen, catalog numbers 61011 and 61012).
Illumina TruSeq stranded total RNA kit (500 ng – 1 µg of RNA)

treatment_protocol: untreated

tag: strain

value: mESC to NPC


title: wt_E12.5_PL_CHIC

description: reanalysis of GSM5034635

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15.
HiCUP [Lieberman-Aiden et al. 2009] version 0.6.1 was used with bowtie2 [Langmead et al. 2012] version 2.2.6 using --re1 '^GATC'  for the digestion and the II1TDOM-542 mutant genome.
BAM was converted to juicebox format with python and bash scripts available at   https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=be5040251cd4afb7&changeset_revision=44365a4feb3b&file_type=gz
Pairs with MAPQ above 30 and where both mates map on chr2 between 72402000 and 77000000 were kept
Pairs were sorted with cooler [https://github.com/open2c/cooler] version 0.7.4 and loaded into a 5kb-binned matrix.
Matrices were then balanced with cooler with parameters: --mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --tol 1e-05 --max-iters 200 --cis-only
Genome_build: II1TDOM-542 mutant genome
Supplementary_files_format_and_content: validpairs are all valid pairs from HiCUP in juicebox format (<readname> <str1> <chr1> <pos1> <frag1>   <str2> <chr2> <pos2> <frag2> <mapq1>   <mapq2> str = strand (0 for forward, anything else for reverse)   pos = middle of the fragment)
Supplementary_files_format_and_content: cool is the balanced matrix at 5kb-bins only in the captured region

growth_protocol: Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.

extract_protocol:
The forelimbs of embryos were dissected into proximal and distal domains, then placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were centrifuged at 300xg for 5 minutes and the supernatant was removed. Cells were then resuspended in ice-cold 1xPBS with PIC and centrifuged again. The cells were then fixed in 1% PFA at room temperuatre for 10 minutes. A final wash was performed and cells were frozen at -80ºC until processing for Hi-C.
Hi-C libraries were processed with the SureSelect XT library preparation kit

value: proximal forelimb

value: wild type


title: SmG6_NPC_d7_Rep2

description:
SmG6_NPC_d7_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

source_name: iXist-ChrX-Cast(mESC)

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating. For NPC differentiation timepoints, mESCs were first extensively separated from feeder cells by pre-plating four times for 35-40 min each. 0.5 x 106 mESCs were then plated to gelatin-coated T25 flasks and grown in N2B27 media (50:50 DMEM/F-12:Neurobasal (Gibco) supplemented with 1 X N2 and 1 X B27 (ThermoFisher), 1 mM L-glutamine, 100 μM β-mercaptoethanol, 50 U/mL penicillin / 50 μg/mL streptomycin (all from Life Technologies) with 1 μg/mL doxycycline for continuous Xist induction.

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1μg/mL) to the culture medium for 1, 3 or 6 days. For FKBP12-PCGF35 lines, dTAG-13 was added at 100uM 12 hours prior to Dox inductiom.

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele); SmcHD1 KO

value: 7 days


title: iXist-ChrX-Cast_ES_d10_Rep3

description:
C7H8_ES_d10r3
iXist-ChrX-Cast_mESC_d10_AllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele)


title: iXist-ChrX-Dom_ES_d10_Rep1

description:
A11B2_ES_d10r1
iXist-ChrX-Dom_mESC_d10_AllelicRatio_table.txt


title: iXist-ChrX-Dom_ES_d10_Rep2

description:
A11B2_ES_d10r2
iXist-ChrX-Dom_mESC_d10_AllelicRatio_table.txt


title: NSH-A_K27M-Tag_H3K4me3_ChIP-seq

value: Neural stem cells

value: Nestin-cre; H3f3aLSL-K27M-Tag/+

value: female


title: iXist-ChrX-Cast_ES_d10_Rep1

description:
C7H8_ES_d10r1
iXist-ChrX-Cast_mESC_d10_AllelicRatio_table.txt


title: iXist-ChrX-Cast_ES_d10_Rep2

description:
C7H8_ES_d10r2
iXist-ChrX-Cast_mESC_d10_AllelicRatio_table.txt


title: SmG6_NPC_d5_Rep1_R2

description:
SmG6_NPC_d5_Rep1_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 5 days


title: SmG6_NPC_d7_Rep1_R2

description:
SmG6_NPC_d7_Rep1_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: wt_E12.5_DFL_ATAC_Bolt2021

description: Reanalyis of GSM5034630

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15.
Reads were mapped with bowtie[Langmead et al. 2012] 2.4.1 with parameters -I 0 -X 1000 --fr --dovetail --very-sensitive on mm10 or on the II1TDOM-542 mutant genome.
Alignments with a mapping quality below 30, discordant pairs, and reads mapping to the mitochondria, were discarded with bamtools version 2.4.0 [https://github.com/pezmaster31/bamtools].
PCR duplicates were removed with Picard[http://broadinstitute.github.io/picard/index.html] version 2.18.2 before the BAM to BED conversion with bedtools[Quinlan et al. 2010] version 2.30.0.
Coverage and peak calling were computed by macs2 [Zhang et al. 2008] version 2.1.1.20160309 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100.
Genome_build: mm10 or the II1TDOM-542 mutant genome
Supplementary_files_format_and_content: bigwig: coverage from macs2
Supplementary_files_format_and_content: narrowPeak: peaks from macs2

extract_protocol:
The forelimbs or forebrains of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were counted and 50,000 cells were isolated for processing with the Nextera Tn5 enzyme (Illumina FC-131-1096) as previously described (Buenrostro NatMeth 2013).
Tn5 treated DNA was amplified with Nextera Library primers using NEBNext library amplification master mix (NEB M0541).

value: distal forelimb


title: SmG6_NPC_d3_Rep2

description:
SmG6_NPC_d3_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 3 days


title: SmG6_NPC_d5_Rep1_R1

description:
SmG6_NPC_d5_Rep1_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast


title: SmG6_NPC_d7_Rep1_R1

description:
SmG6_NPC_d7_Rep1_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: SmG6_NPC_d3_Rep1_R1

description:
SmG6_NPC_d3_Rep1_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: SmG6_NPC_d3_Rep1_R2

description:
SmG6_NPC_d3_Rep1_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: SmG6_NPC_d35_Rep2_R1

description:
SmG6_NPC_d35_Rep2_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: NPC

value: 35 days


title: SmG6_NPC_d2_Rep2

description:
SmG6_NPC_d2_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Female

value: 2 days


title: iXist-ChrX-Dom_ES_0h_mRNA_Rep2

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (Dom/129S allele)


title: SmG6_NPC_d5_Rep2

description:
SmG6_NPC_d5_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: wt_E12.5_DL_CHIC

description: reanalysis of GSM5034636

value: wild type


title: iXist-ChrX-Dom_ES_d10_Rep3

description:
A11B2_ES_d1r3
iXist-ChrX-Dom_mESC_d10_AllelicRatio_table.txt

value: mESC

value: 10 days


title: SmG6_NPC_d35_Rep2_R2

description:
SmG6_NPC_d35_Rep2_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele); SmcHD1 KO


title: SmG6_NPC_d21_Rep2

description:
SmG6_NPC_d21_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 21 days


title: SmG6_NPC_d15_Rep1

description:
SmG6_NPC_d15_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 15 days


title: SmD5_NPC_d7_Rep1_R2

description:
SmD5_NPC_d7_Rep1_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 7 days


title: SmG6_NPC_d2_Rep1

description:
SmG6_NPC_d2_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: SmD5_NPC_d7_Rep2

description:
SmD5_NPC_d7_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: shPAB polysomal fraction 5 [shPAB-F5]

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description:
stable shRNA expression
SH81_5_S5_L003

data_processing:
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.4) with default settings.
RNASeq reads’ alignment was performed using STAR (v2.6.0c) with the GRCh38 reference genome without alternative contigs.
Ensembl gene annotation v94 was used for both transcript expression quantification and the identification of 3’-UTR regions
Transcript quantification was performed using StringTie (1.3.4d) with the "-e" mode to only quantify the expression of known transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: transcript_level_tpm.tsv.gz, TPM counts of all annotated transcripts

source_name: shPAB polysomal fraction

growth_protocol: Cell growth is described in PMCID: PMC3824410

extract_protocol:
poysomal fractionation was carried out as desribed in PMID: 28516123.
rRNA depletion was carried out with the NEBnext rRNA depletion kit (NEB), liberary was contructed with random hexamers and superscript III (ThermoFisher Scientific)
Prior to sequencing (Illumina HiSeq4000 2x150bp 30Mreads depth), cDNA samples from the sucrose gradient were pooled: F3= F3+F4; F4=F5+F6+F7; F5=F8-F11. RNA and cDNA were assessed using bioanalyzer 2100 (Agilent).

treatment_protocol: Generation of shPAB and control are described in PMCID: PMC3824410

value: immortalized, 7304.1

value: muscle cell line

tag: genotype/variration

value: shRNA to PABPN1 (sh81)


title: shPAB polysomal fraction 4 [shPAB-F4]

description:
stable shRNA expression
SH81_4_S4_L003


title: SmG6_ES_Rep1

description:
SmG6_ES_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast


title: S075 [206339210076_R07C01]

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using the minfi package running on RStudio version 1.4.1717 based on the statistical language R version 4.1.1
The 'bVals_matrix.csv' contains average beta-Values after normalization using the Noob method

label: Cy5 and Cy3

source_name: specimen

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

value: male

tag: age

tag: diagnosis

value: Chronic pleuritis


title: S074 [206339210076_R06C01]


title: SmD5_NPC_d7_Rep1_R1

description:
SmD5_NPC_d7_Rep1_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Female


title: S073 [204776830115_R08C01]

value: Mesothelioma, biphasic


title: SmD5_NPC_d5_Rep1_R2

description:
SmD5_NPC_d5_Rep1_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: mESC to NPC

value: 5 days


title: SmD5_NPC_d3_Rep2

description:
SmD5_NPC_d3_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 3 days


title: S071 [204776830115_R03C01]


title: shPAB polysomal fraction 2 [shPAB-F2]

description:
stable shRNA expression
SH81_2_S2_L003

tag: cell line


title: S072 [204776830115_R06C01]


title: SmD5_NPC_d5_Rep1_R1

description:
SmD5_NPC_d5_Rep1_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: SmD5_NPC_d3_Rep1_R2

description:
SmD5_NPC_d3_Rep1_R2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: S069 [204776830106_R06C01]

value: Lung adenocarcinoma, pleural carcinosis


title: S068 [204776830106_R03C01]


title: Parental polysomal fraction 5 [P-F5]

description:
control line
CTRL_5_S10_L003

source_name: Parental polysomal fraction

value: parental


title: S070 [204776830106_R08C01]


title: shPAB polysomal fraction 1 [shPAB-F1]

description:
stable shRNA expression
SH81_1_S1_L003


title: SmD5_NPC_d35_Rep2

description:
SmD5_NPC_d35_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele); SmcHD1 KO

value: 35 days


title: S067 [204776830081_R08C01]

value: Mesothelioma, sarcomatoid


title: SmD5_NPC_d3_Rep1_R1

description:
SmD5_NPC_d3_Rep1_R1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: SmD5_NPC_d5_Rep2

description:
SmD5_NPC_d5_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: S076 [206339210076_R08C01]


title: S066 [204776830081_R07C01]


title: SmD5_NPC_d2_Rep2

description:
SmD5_NPC_d2_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 2 days


title: S065 [204776830081_R06C01]


title: shPAB polysomal fraction 3 [shPAB-F3]

description:
stable shRNA expression
SH81_3_S3_L003

value: immortalized, 7304.1

value: muscle cell line


title: S064 [204776830081_R05C01]


title: S063 [204776830081_R04C01]

value: female


title: SmD5_NPC_d2_Rep1

description:
SmD5_NPC_d2_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast


title: Parental polysomal fraction 2 [P-F2]

description:
control line
CTRL_2_S7_L003


title: S061 [204776830081_R02C01]


title: S062 [204776830081_R03C01]

value: male


title: Parental polysomal fraction 1 [P-F1]

description:
control line
CTRL_1_S6_L003


title: SmD5_NPC_d21_Rep2

description:
SmD5_NPC_d21_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Female

value: 21 days


title: S059 [204776830051_R08C01]


title: S060 [204776830081_R01C01]


title: SmD5_NPC_d15_Rep1

description:
SmD5_NPC_d15_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: 15 days


title: ST_1002

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

institute: Northwestern University

data_processing:
Sequencing adapters were removed with trimmomatic v0.39 and low-quality reads were filtered with the tool’s default settings (leading:3, trailing:3, slidingwindow:4:15).
Filtered reads were aligned with kallisto v0.48.0 to Rattus norvegicus genome release 105 (http://ftp.ensembl.org/pub/release-105/fasta/rattus_norvegicus/cdna/).
Expression values were calculated with tximport v1.22.0
Assembly: Rattus norvegicus genome release 105
Supplementary files format and content: Matrix with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix with raw transcript counts for every sample
Supplementary files format and content: Matrix witnormlized gene counts (tpm) for every gene and every sample
Supplementary files format and content: Matrix with raw transcript counts (tpm) for every\every sample

source_name: Rat heart

growth_protocol: 1-week-old male Sprague-Dawley rat pups underwent an ascending aortic constriction that led to the development of left ventricular hypertrophy by 10 weeks of age.

extract_protocol:
Explanted rat hearts were arrested with the cardioplegic solution. Tissues (~5mg) were collected from inferior and superior sinoatrial nodefrom the left and right atria,  and left ventricles. The tissue was stored in RNAlater (Invitrogen) overnight at +4 °C and  stored at -80 °C. Total mRNA was extracted with RNeasy Micro Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
TruSeq RNA Library Prep Kit (Illumina)

tag: cardiac chamber

value: Superior sino-atrial node

value: Male

value: 10 weeks

tag: health state

value: healthy

value: Sprague-Dawley rat


title: Parental polysomal fraction 4 [P-F4]

description:
control line
CTRL_4_S9_L003

value: parental


title: S058 [204776830051_R07C01]

tag: gender

value: Mesothelioma, epitheloid


title: S056 [204776830051_R05C01]


title: S055 [204776830051_R02C01]


title: ST_0921


title: SmD5_ES_Rep2

description:
SmD5_ES_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: mESC

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele); SmcHD1 KO


title: S057 [204776830051_R06C01]


title: Parental polysomal fraction 3 [P-F3]

description:
control line
CTRL_3_S8_L003

value: immortalized, 7304.1


title: ST_1001


title: S053 [204776830025_R03C01]

value: Mesothelioma, biphasic


title: SmA3_NPC_d7_Rep2

description:
SmA3_NPC_d7_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); SmcHD1 KO

value: 7 days


title: SmD5_ES_Rep1

description:
SmD5_ES_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast

value: Female


title: ST_0920


title: S054 [204776830025_R08C01]

value: male


title: SmA3_NPC_d7_Rep1

description:
SmA3_NPC_d7_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt


title: sSAN0508

value: Superior sino-atrial node

value: failing


title: BA treatment 24hpi not infecting rep2

city: UPPSALA

first: Anna

last: Kokla

state: Select

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
BA_24_U_2

data_processing:
adapter and low-quality sequences were removed using the fastp software
The quality-filtered reads were mapped to both the Phtheirospermum  and Arabidopsis genome (TAIR10) using STAR and were separated based on mapping to Phtheirospermum and Arabidopsis reads.The separated reads were then re-mapped to their respective genomes.
The raw read count was calculated using FeatureCounts
The differential expression analysis was performed using Deseq2
Genome_build: Pjv1 for Phtheirospermum and TAIR 10 for Arabidopsis
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism:
Arabidopsis thaliana
Phtheirospermum japonicum

source_name: Root

growth_protocol: Phtheirospermum and Arabidopsis seeds were surface sterilized with ethanol, plated on 1/2MS+1%sucroze+0.8%plantagar plates and stratified for 2 days. Seedlings were grown for 4 days in long day conditions, 16h light (25 C) and 8h darkness (25 C) at light intensity of 100µE/m2/s.

extract_protocol:
Total RNA was extracted using the ROTI®Prep RNA MINI (Roth) kit
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® for paired end sequencing

treatment_protocol: Phtheirospermum seedlings were transferred to 0.8% plant agar plates containing DMSO or 10.3mM ammonium nitrate or 80nM 6-Benzylaminopurine for 3 days prior to the Arabidopsis addition (infecting samples). Arabidopsis and Phtheirospermum were transferes in the same treatments but separetely for the not infecting samples. 40 plants were used per sample. The 2mm root tip (0hpi samples and not infecting samples) or the haustorium formation site +/- 2mm above and below were harvested (infecting samples) for both Phtheirospermum and Arabidopsis.

value: Phtheirospermum Okayama anr Arabidopsis Col-64

value: root tissue including the haustorium formation site and 1-2 mm above and below it

tag: treatment

tag: time

value: Arabidopsis at 24hpi


title: BA treatment 24hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
BA_24_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-63


title: S051 [204776820028_R08C01]

value: Chronic pleuritis


title: sSAN0507

value: Male

value: 10 weeks

value: Sprague-Dawley rat


title: S052 [204776820046_R04C01]


title: S050 [204776820028_R07C01]


title: SmA3_NPC_d5_Rep2

description:
SmA3_NPC_d5_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: 5 days


title: SmA3_NPC_d5_Rep1

description:
SmA3_NPC_d5_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC


title: BA treatment 24hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
BA_24_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-62


title: S049 [204776820028_R03C01]


title: sSAN0506


title: SmA3_NPC_d52_Rep1

description:
SmA3_NPC_d52_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); SmcHD1 KO

value: 52 days


title: sSAN0409


title: BA treatment 24hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
BA_24_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-61


title: BA treatment 24hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
BA_24_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-60


title: SB_1002

value: Inferior sino-atrial node

value: healthy


title: S047 [204674430006_R07C01]

value: male

value: Mesothelioma, sarcomatoid


title: S048 [204776820023_R01C01]


title: SmA3_NPC_d3_Rep2

description:
SmA3_NPC_d3_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast

value: Female

value: 3 days


title: BA treatment 24hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
BA_24_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-65

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 24hpi


title: SmA3_NPC_d3_Rep1

description:
SmA3_NPC_d3_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC


title: SmA3_NPC_d35_Rep1

description:
SmA3_NPC_d35_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: 35 days


title: SB_1001

value: Male

value: 10 weeks

value: Sprague-Dawley rat


title: S046 [204674430006_R06C01]


title: BA treatment 12hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
BA_12_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-58

value: Arabidopsis at 12hpi


title: SB_0921

value: Inferior sino-atrial node


title: SmA3_NPC_d2_Rep2

description:
SmA3_NPC_d2_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); SmcHD1 KO

value: 2 days


title: BA treatment 12hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
BA_12_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-59