title: Striatum P7, run 1

description:
PN1
LAT293A3
PN1_L1


title: Striatum 3m, repl 1, run 4

status: Public on Jun 11 2020

type: SRA

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description:
WT1
LAT293A1
WT1_L4

library_source: transcriptomic

data_processing:
The resulting data was demultiplexed using the 10x cellranger mkfastq function according to manufactuer’s instructions. Reads from individual samples were mapped to the mouse genome (mm10) and quantified with the cell ranger count function (v3.0.2, option --expect-cells=3500).
The generated count matrices were imported into Seurat (v3.1.1) (Stuart et al., 2019) and aggregated using the Seurat “merge” function.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts for each gene for each cell; cells from all samples merged (extracted from Seurat)

molecule: polyA RNA

organism: Mus musculus

source_name: striatal astrocytes (MACS-purified)

extract_protocol:
cell suspensions of striatal astrocytes were prepared by anti-ACSA2-MACS. Samples were prepared using the 10x Chromium Next GEM Single Cell 3ʹ v3.1 kit.
Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions.
scRNA-Seq

tag: strain

value: mixed

tag: tissue

value: striatum

tag: age

value: 3 months

tag: genotype

value: wild type

tag: cell type

value: striatal astrocytes (MACS-purified)

tag: experimental group


title: Striatum 3m, repl 1, run 3

description:
WT1
LAT293A1
WT1_L3


title: Breast cancer PD35987a

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulfite-converted genomic DNA was hybridised to Illumina EPIC 850K arrays using standard manufacturer protocols

scan_protocol: Standard Illumina scanner and settings

data_processing: Raw signal values extracted using minfi::preprocessRaw() followed by minfi::getUnmeth and minfi::getMeth. Normalized betas were obtained by minfi::preprocessFunnorm(), betas were then scaled to adjust for difference in Infinium I/II beta distribution using the method of Karlsson et al. 2014 (PMID: 25278450), finally Zhou et al. 2016 (PMID: 27924034) annotations (20180909 data freeze) were used to filter out unreliable probes.

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast cancer

label_protocol: Standard Illumina protocol

extract_protocol: Standard DNA extraction protocol according to SCAN-B workflow

tag: subtype

value: TNBC

value: Hypermethylated

tag: gender

value: female


title: RDRP1 mutant strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, second duplicate

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

country: Spain

institute: Universidad de Murcia

data_processing:
Data filtering by FASTQC and Trim Galore!
Read alignment by STAR
Differential expression analyses by limma
Genome_build: Mucor circinelloides f. lusitanicus CBS277.49 v2.0 (JGI)
Supplementary_files_format_and_content: Gene differential expression analysis table from limma

organism: Mucor lusitanicus

source_name: Fungal spore-macrophage coculture

growth_protocol: culture duration: 5 hours. L15 cell culture medium

extract_protocol:
Cultures were frozen with liquid nitrogen and grinded into dust. Total RNA was extracted using RNeasy® Plant Mini Kit (Qiagen, Hilden, Germany) following the supplier’s recommendations
mRNA enrichment by poly (A) purification capture and cDNA libraries were prepared at BaseClear (Leiden, The Netherlands) using TruSeq RNA Library preparation kits

value: RDRP1 mutant

tag: culture duration

value: 5 hours

tag: culture type

value: coculture with Mus musculus

tag: fungal parental strain

value: Mucor circinelloides f. lusitanicus MU402


title: wt_chlor_15

city: Cambridge

first: Michele

last: LeRoux

state: MA

address: 31 Ames St

department: Biology

country: USA

institute: MIT

description: RNA with rRNA subtracted

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment a count was added at all aligned positions.
Counts were depth normalized to a pseudo-reference sample calculated from all samples
Counts at all positions were log2 transformed and a ratio was calculated (wildtype - ∆10TA) for assessing toxin activity.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: chlor_15_ratio.csv.gz, chlor_30_ratio.csv.gz, and chlor_60_ratio.csv.gz are log-transformed lists of sequencing depth-normalized counts for every genomic position at both strands for each time point. The files contain 2 rows by 4639675 columns where the first row is the positive strand and the second row is the negative strand.

molecule: total RNA

organism: Escherichia coli

source_name: Bacterial liquid culture

growth_protocol: Overnight cultures of E. coli MG1655 wildtype or ∆10TA (Goeders, Dreze, Van Melderen 2013 J. Bacteriology) were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.3 at 37°C in an orbital shaker at 200 RPM. Chloramphenicol was added to a final concentration of 75 µg/mL. Cells were collected for RNA extraction at 15, 30, and 60 min after addition of chloramphenicol.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, samples were treated with bacterial Ribo-Zero kit (Illumina) and the resulting RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were size selected and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

treatment_protocol: Chloramphenicol was added to all cultures to a final concentration of 75 µg/mL.

tag: time point (minutes)


title: Striatum 3m, repl 1, run 2

description:
WT1
LAT293A1
WT1_L2


title: RDRP1 mutant strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, first duplicate


title: R3B2 mutant strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, second duplicate

value: R3B2 mutant


title: Tnaive H m6A input

city: Chciago

first: Chuan

last: He

state: IL

address: 929 E 57 th St

institute: University of Chicago

data_processing:
Library strategy: MeRIP-seq
Base-calling performed using CASAVA
Reads were aligned to the mouse transcriptome mm10 using hisat2 (v2.1.0)
m6A peaks are called by RADAR
Genome_build: mm10
Supplementary_files_format_and_content: Treg_Tnaive_m6A.xls and GF_SPF_m6A.xls contain the differentially methylated peaks between indicated cell types called by RADAR

source_name: T Cells

growth_protocol: CD4 + Tnaïve cells were cultured in Advanced RPMI 1640 + 10% FBS + 1% penicillin/streptomycin + 2mM L-glutamine + 20 ng/mL TGFb + 40 ng/mL IL-2 + 1nM all-trans-retinoic-acid for 96 hours to generate induced Treg

extract_protocol:
RNA was isolated with the Trizol reagent and Direct-zol RNA Kit. polyA RNAs were enriched with Dynabeads mRNA Purification Kit and fragmented to 150 nt with a Bioruptor Pico sonicator. 4% fragmented RNA was saved as input. Remaining fragments containing m6A were enriched with the EpiMark N6-methyladenosine Enrichment Kit.
All libraries were constructed with the SMARTer Stranded Total RNA-Seq Kit v2 (Takara)

value: Tnaive

tag: mouse facility

value: Specific pathogen free

tag: antibody

value: none (input)


title: R3B2 mutant strain cocultured with mouse macrophages (cell line J774A.1) for 5 hours, first duplicate


title: Breast cancer PD35962a


title: Breast cancer PD35982a


title: Breast cancer PD35984a


title: Astr in vitro, prep X9, 3D, BMP 7d, FGF2 7d [RNA-Seq]

description:
LAT348A12
X9_3D_FGF_1
RNA_deseq_results_maturation_conditions.csv

data_processing:
Reads from RNA-Seq fastq files were aligned to the mm10 genome and quantified using the crickbabs/BABS-RNASeq nextflow pipeline (https://github.com/crickbabs/BABS-RNASeq; git commit id: 335ce47db079d6cc2a7f82f4b762620c4f7f27e2). The pipeline was run using nextflow version 0.30.2 (Di Tommaso et al., 2017) with the command “nextflow run main.nf -params-file params.yml”.
Downstream analysis with Bioconductor “DESeq2” package (v1.24.0)
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene, DESeq2 results: normalised expression and statistics; cortical in vivo samples included

source_name: in vitro differentiated astrocytes

extract_protocol:
RNA was extracted using Trizol, from frozen pellets of MACS-purified astrocytes, or by direct lysis of cultured cells on culture dishes. The “Direct-zol RNA MiniPrep Kit” (Zymo Research, R2052) was used for purification of the extracted RNA, according to manufacturer’s instructions, including the optional Dnase digestion step.
RNA was prepared into cDNA using the NuGEN Ovation RNA-Seq System V2 kit (Tecan). Following cDNA generation, cDNA was fragmented to an average length of 300 bp using the Covaris E220 focused ultrasonicator (Covaris).  Final libraries were then prepared using the NuGEN Ovation Ultralow Library System V2 (Tecan) according to the manufactuer’s instructions.

value: cortical grey matter

value: post natal day 3

value: in vitro differentiated astrocytes

tag: treatment

value: FGF medium, 3D culture


title: Astr in vitro, prep X9, 3D, BMP 7d, basal 7d [RNA-Seq]

description:
LAT348A11
X9_3D_bas_1
RNA_deseq_results_maturation_conditions.csv

value: mixed

value: wild type

value: basal medium, 3D culture


title: RDRP1 mutant strain singlecultured in cell media for 5 hours, first duplicate

source_name: Fungal spores

value: single


title: Breast cancer PD35972a

value: TNBC

value: Hypermethylated

value: female


title: Breast cancer PD35979a


title: Astr in vitro, prep X8, 3D, BMP 7d, FGF2 7d [RNA-Seq]

description:
LAT348A8
X8_3D_FGF_1
RNA_deseq_results_maturation_conditions.csv


title: Breast cancer PD35980a


title: Breast cancer PD35957a


title: RDRP1 mutant strain singlecultured in cell media for 5 hours, second duplicate

value: RDRP1 mutant

value: 5 hours


title: R3B2 mutant strain strain singlecultured in cell media for 5 hours, second duplicate

value: R3B2 mutant

value: Mucor circinelloides f. lusitanicus MU402


title: Astr in vitro, prep X6, 3D, BMP 7d, FGF2 7d [RNA-Seq]

description:
LAT348A4
X6_3D_FGF_1
RNA_deseq_results_maturation_conditions.csv

value: subventricular zone

value: 2 months


title: Astr in vitro, prep X6, 3D, BMP 7d, basal 7d [RNA-Seq]

description:
LAT348A3
X6_3D_bas_1
RNA_deseq_results_maturation_conditions.csv


title: Astr in vitro, prep X9, BMP 7d, FGF2 7d [RNA-Seq]

description:
LAT348A10
X9_2D_FGF_2
RNA_deseq_results_maturation_conditions.csv

value: cortical grey matter

value: FGF medium, 2D culture

value: FGF


title: PAR1006 input

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

library_source: genomic

data_processing:
Fastq files were trimmed from adapters using cutadapt (options: -q 20 -O 3 http://dx.doi.org/10.14806/ej.17.1.200, ver: 1.16) and aligned32 to a combined genome consisting of hg19 (H. Sapiens), dm6 (D. melanogaster) and mm10 (M.musculus) with bwa-mem (ver. 0.7.17-r1188). Bam files were generated from the alignment with samtools view (options: -Sb -F2308 -q 10, ver: 1.9) and subsequently split by organisms to obtain 3 bam files for each sample.
Duplicated reads were marked and removed using picard MarkDuplicates (ver: 2.20.3).
For all organisms, the total sequencing coverage (total recovery) was quantified as the total number of unique reads aligning to the respective genome
Standard peak calling was performed for each sample using MACS2 (ver. 2.1.2) with default options on hg19 and dm6 bam files respectively.
For each human PDTX model, peak regions were considered positive if confirmed in 2 out of 4 technical replicates (multi2) with bedtools v2.27.1 multiinter. All human confirmed G4-ChIP-seq peak files (multi2) of the 22 models were merged (bedtools merge) and regions more than 99 bp long retained to generate a single G4 DNA consensus of 26,103 G4 regions. Finally, the coverage of the samples was quantified over the consensus human set (bedtools coverage).
Reference normalization factor estimation and human ChIP signal normalization. For each PDTX biopsy, four technical qG4-ChIP experiments were performed and sequenced alongside one input chromatin (control). In each experiment, a similar amount of reference (D. melanogaster) chromatin from the same batch was added. To estimate PDTX normalization factors, reference coverage was determined at a pre-defined consensus consisting of 1,367 intervals (see Supplementary Data 2). The reference consensus set was defined from, and covers, G4-enriched regions observed in more than 110 pull-down experiments. The normalization factor of each ChIP sample has been defined as the ratio between the maximum observed coverage (across all ChIP samples) and the individual sample coverage. Note that only ChIP experiments were used for this step (i.e. inputs are excluded and forced to 1). . The normalization factors were then exported and used as input for a customized R script performing the normalization of the human signal. For each G4-ChIP-seq experiment, human signal (i.e. read coverage within human G4 consensus) was quantified by performing input subtraction and normalization with their respective reference reads and human library sizes. To assess if the normalization step has globally improved the experimental reproducibility, a quantitative parameter, the Improvement Factor IF, was devised that measures both the increase (i.e. improvement) in data similarity  between experiments corresponding to the same technical and biological samples and the increase dissimilarity between different samples. Specifically, the improvement factor of each biological sample has been estimated as: IF = sum_N(D_ratio_inter) - sum_N(D_ratio_intra).  Where: o  D_ratio: euclidean_distance_after_normalization/euclidean_distance_before_normalization;  o  N: total N. ChIP samples  o  euclidean_distance_after_normalization: Euclidean similarity matrix computed on input  subtracted, library size adjusted, drosophila normalized data and rescaled to its  maximum value;  o  euclidean_distance_before_normalization: Euclidean similarity matrix computed on input  subtracted, library size adjusted data and rescaled to its maximum value;   o  D_ratio_inter: similarity values among samples belonging to the same technical or  biological group;   o  D_ratio_intra: similarity values among samples not belonging to the same  technical or biological group;   135 individual samples (ChIP + Input) were processed from 22 different PDTX models. Some   PDTX models have more than one biological sample.
Genome_build: hg19, dm6, mm10
Supplementary_files_format_and_content: bigwig files  *nodup.w10.rpm.bw were generated from the duplicates removed bam files binning the regions in 10bp windows and normalizing the coverage in those regions by the total number of unique reads. The bigwig files *nodup.dm6.sorted.bw were generated starting from **nodup.w10.rpm.bw and following those steps: 1. bw converted to begraph; 2.using bedtools unionbedg  perform input subtraction (pull-down minus input RPM) and multiply by drosophila normlization factors.

organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

source_name: fixed human breast cancer PDTX tissue

extract_protocol:
PDTX chromatin prep and G4-ChIP-seq: Briefly, D. melanogaster S2 cells were cultured in Schneider's Drosophila Medium (Thermo Fisher Scientific, cat no. R69007) containing 10% fetal bovine serum (FBS) Medium (Thermo Fisher Scientific, cat no. 10500064). To prepare spike-in Drosophila chromatin, 100 million cells were i) harvested by centrifugation, ii) fixed for 10 min in a solution of media containing 10 % FBS, 1% Formaldehyde (Thermo Fisher Scientific, cat no. 28908) and iii) quenched for 5 min by addition of 125 mM glycine (Fisher Scientific, cat no. 11545005). The cell pellet was washed with 10 mL PBS, pelleted by centrifugation and subsequently stored on ice for the lysis procedure. The 2-step chromatin lysis procedure was performed according to the Chromatrap procedure ("Spin column ChIP kit for qPCR v6.4"). 500 µL intact chromatin was sonicated into 100-500 bp fragments using a Bioruptor Plus (Diagenode cat. no. B02010003 with cooling) at 4C. Sonicated chromatin was diluted with 1.5 mL lysis buffer (Chromatrap cat no. 100005) before snap-freezing as 25 µL aliquots. PDTX chromatin was prepared essentially as described in Schmidt et al. (Methods 2009)30. Briefly, a snap-frozen PDTX biopsy, ~1 cm3, was transferred into a 50 mL falcon tube, on dry-ice, and crushed into smaller chunks on dry-ice using a scalpel followed by fixation for 20 min in 30 ml solution A, containing 1% formaldehyde, and then quenched for 5 min by adding 125 mM glycine. The supernatant of the pelleted tissue was discarded, and the pellet washed twice with 10 mL ice-cold PBS before resuspending in 1 mL PBS and transferred to a 1 mL glass Douncer (Fisher scientific, cat no. 11591295). 10 strokes were employed for each douncing step with a loose and then tight pestle, and the remaining tissue slurry was transferred to a 15 mL tube, centrifuged for 5 min at 2500xg and subjected to lysis according to Schmidt et al30. Briefly, after the 10 mL LB2 treatment and nuclei pelleting step, the pellet was resuspended in 500 µL LB3 and LB3-chromatin solution split into two Bioruptor TBX (Diagenode, cat no. C30010010-300) sonication tubes. The samples were sonicated until the desired fragment length (100-500 bp) was achieved. Finally, 50 µL of a 10% Triton X-100 LB3 solution was mixed with the sonicated solution and aliquoted into 50 µL aliquots before snap-freezing in liquid nitrogen. 5 μL of PDTX chromatin was quantified by Qubit using the "broad range kit" (Thermo Fisher Scientific, cat. no. Q32853). In each qG4-ChIP-seq reaction, 225ng of PDTX chromatin, 102ng of spike-in drosophila chromatin and 2% RNaseA (Invitrogen, cat. no. AM2271) in blocking buffer (25mM HEPES, pH 7.5, 10.5mM NaCl, 110mM KCl, 1mM MgCl2 and 1% BSA (Merck, cat. no. A7030) in Milli-Q water were mixed and incubated at 37C for 30min at 800rpm. All PDTX chromatin batches containing a different concentration than 30 ng/μL were balanced to the same level, either by dilution with LB3 containing 1% Triton X-100 or by up-scaling the ChIP reaction. For PDTX chromatin with a concentration of 30 ng/μL, 7.5 μL of the PDTX chromatin was added to a solution containing 270 μL blocking buffer including 2% RNase A and 7.5 μL spike-in drosophila chromatin. After RNaseA treatment, 15 μL of 2M BG4, prepared as described previously31, was added to each qG4-ChIP-seq reaction and the reaction mixture shaken at 1,400 rpm at 16C for 1 hour. Meanwhile, 65 μL of anti-FLAG magnetic beads (Sigma-Aldrich, cat. no. M8823) were washed three times with 650 μL of blocking buffer and resuspended in 1,300 μL blocking buffer. The pre-washed beads were incubated at 16C at 1,400rpm and 300 μL of pre-washed beads added to the reaction mixture after BG4 incubation. The reaction mixture with beads was incubated at 16C for 1 hour at 1,400rpm. Then, the beads were washed four times in 400 μL cold wash buffer (100mM KCl, 0.1% Tween 20 and 10mM Tris, pH 7.4 in Milli-Q water) in the cold room and twice at 37C for 15min at 1,400rpm, followed by one cold wash on magnetic stand. The enriched chromatin on beads was resuspended in 75 μL TE buffer and 1 μL Proteinase K (Invitrogen, cat. no. AM2546) added. 6 μL Proteinase K was added to input sample which refers to a qG4-ChIP-seq reaction mixture without BG4 and beads. The reaction mixture was incubated at 65C for 3 hours at 1,400 rpm and purified using QIAGEN MinElute Kit (QIAGEN, cat. no. 28206).
Purified DNAs were subjected to Nextera DNA library preparation.For 40 μL library preparation reaction, 3-5ng of the ChIP or input DNA (Qubit high sensitivity kit, Thermo Fisher Scientific, cat. no. Q32854), 20 μL 2X tagmentation buffer (Illumina, cat. no. 15027866), 1.25 μL Tn5 enzyme (Illumina, cat no. 18027865) and nuclease-free water was incubated at 37°C for 20min at 800rpm. The reaction mixture was purified using QIAGEN MinElute Kit (QIAGEN, cat. no. 28206) according to the manufacturer’s instruction and eluted in 20 μL EB buffer. To amplify the library, 20 μL of the DNA was then mixed with 25 μL NEB Next High Fidelity 2X PCR Master Mix (New England Biolabs, cat. no. N0541S), 2.5 μL Nextera index kit i5 primer (Illumina, cat. no. 15055290) and 2.5 μL Nextera index kit i7 primer (Illumina, cat. no. 15055290). The PCR program was as follows: 72°C for 5 minutes, 98°C for 30 seconds, followed by 8 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Libraries were quantified using a Bioanalyzer (Agilent) to estimate the average library size and concentration determined via Qubit HS. The library concentration was corrected for the library size using the following relationship:1 ng/µL = 3nM = 500 bp. Samples were subjected to single-end sequencing with a read length of 75bp on an Illumina NextSeq instrument.”

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

tag: chip antibody

value: BG4 single-chain antibody

tag: spike-in reference organsms

value: Drosophila melanogaster

tag: spike-in cell line

value: Drosophila S2 cells


title: Astr in vitro, prep X8, BMP 7d, FGF2 7d [RNA-Seq]

description:
LAT348A6
X8_2D_FGF_1
RNA_deseq_results_maturation_conditions.csv

tag: strain

value: mixed

tag: tissue

value: post natal day 3

value: wild type

value: in vitro differentiated astrocytes


title: PAR1006 rep3


title: Striatum 3m, repl 1, run 1

description:
WT1
LAT293A1
WT1_L1

value: striatum

tag: age

value: 3 months

tag: genotype

value: striatal astrocytes (MACS-purified)


title: PAR1006 rep4

tag: cell type


title: Breast cancer PD35999a

tag: subtype

value: TNBC

value: Hypermethylated

value: female


title: Breast cancer PD35954a

tag: gender


title: Breast cancer PD35996a


title: Breast cancer PD35945a


title: Breast cancer PD35985a


title: Breast cancer PD35946a


title: Breast cancer PD35939a


title: Breast cancer PD35941a


title: Astr in vitro, prep X6, BMP 7d, FGF2 7d [RNA-Seq]

description:
LAT348A2
X6_2D_FGF_1
RNA_deseq_results_maturation_conditions.csv

value: subventricular zone

value: 2 months

value: FGF medium, 2D culture

tag: experimental group


title: Breast cancer PD35955a


title: Breast cancer PD35953a


title: Breast cancer PD35935a


title: Astr in vitro, prep X8, BMP 7d, basal 7d [RNA-Seq]

description:
LAT348A5
X8_2D_Bas_1
RNA_deseq_results_maturation_conditions.csv

value: cortical grey matter

value: basal medium, 2D culture

value: Control(basal 2D)


title: PAR1006 rep1

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody

value: Drosophila melanogaster

value: Drosophila S2 cells


title: PAR1006 rep2


title: Astr in vitro, prep X9, BMP 7d, basal 7d [RNA-Seq]

description:
LAT348A9
X9_2D_bas_1
RNA_deseq_results_maturation_conditions.csv

value: mixed

value: post natal day 3

value: wild type

value: in vitro differentiated astrocytes


title: Astr in vitro, prep X8, 3D, BMP 7d, basal 7d [RNA-Seq]

description:
LAT348A7
X8_3D_bas_1
RNA_deseq_results_maturation_conditions.csv

value: basal medium, 3D culture


title: STG195M input


title: R3B2 mutant strain strain singlecultured in cell media for 5 hours, first duplicate

value: R3B2 mutant

tag: culture duration

value: 5 hours

tag: culture type

value: single

value: Mucor circinelloides f. lusitanicus MU402


title: Breast cancer PD35926a

value: TNBC

value: Hypermethylated

value: female


title: STG195M rep4

value: breast cancer tissue


title: Astr in vitro, prep X9, Rorb and Fezf2 [RNA-Seq]

description:
LAT585A6
X9B_RF_5
RNA_deseq_results_Rorb_Fezf2_combined_OE.csv

value: cortical grey matter


title: Astr in vitro, prep X8, Rorb and Fezf2 [RNA-Seq]

description:
LAT585A5
X8B_RF_5
RNA_deseq_results_Rorb_Fezf2_combined_OE.csv


title: Breast cancer PD35938a


title: STG195M rep3

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody


title: Astr in vitro, prep X6, Rorb and Fezf2 [RNA-Seq]

description:
LAT585A4
X6B_RF_5
RNA_deseq_results_Rorb_Fezf2_combined_OE.csv

value: subventricular zone

value: 2 months


title: STG195M rep2

value: Drosophila melanogaster

value: Drosophila S2 cells


title: STG195M rep1


title: AB790 input


title: Breast cancer PD35932a


title: Astr in vitro, prep X8, Fezf2 [RNA-Seq]

description:
LAT172A20
X8B_Fezf2_3
RNA_deseq_results_TF_OE.csv

value: mixed

value: post natal day 3

value: in vitro differentiated astrocytes


title: AB790 rep4


title: AB790 rep3


title: Breast cancer PD31171a


title: Astr in vitro, prep X9, Lhx2 [RNA-Seq]

description:
LAT172A23
X9B_Lhx2_4
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD35929a


title: Astr in vitro, prep X6, Fezf2 [RNA-Seq]

description:
LAT172A16
X6B_Fezf2_3
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD31175a


title: Astr in vitro, prep X6, Lhx2 [RNA-Seq]

description:
LAT172A15
X6B_Lhx2_3
RNA_deseq_results_TF_OE.csv


title: AB790 rep1


title: Astr in vitro, prep X8, Lhx2 [RNA-Seq]

description:
LAT172A19
X8B_Lhx2_3
RNA_deseq_results_TF_OE.csv


title: Astr in vitro, prep X9, Dbx2 [RNA-Seq]

description:
LAT172A11
X9B_Dbx2_1
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD31178a


title: Breast cancer PD35986a


title: STG282M rep4


title: STG282M rep3


title: Astr in vitro, prep X8, Dbx2 [RNA-Seq]

description:
LAT172A7
X8B_Dbx2_1
RNA_deseq_results_TF_OE.csv


title: Astr in vitro, prep X6, Dbx2 [RNA-Seq]

description:
LAT172A4
X6B_Dbx2_2
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD31169a


title: STG282M input


title: Astr in vitro, prep X9, Rorb [RNA-Seq]

description:
LAT172A22
X9B_Rorb_3
RNA_deseq_results_TF_OE.csv

value: Rorb


title: Breast cancer PD31176a


title: STG282M rep1


title: Breast cancer PD31158a


title: Astr in vitro, prep X8, Rorb [RNA-Seq]

description:
LAT172A18
X8B_Rorb_3
RNA_deseq_results_TF_OE.csv


title: STG282M rep2


title: Astr in vitro, prep X9, Fezf2 [RNA-Seq]

description:
LAT172A24
X9B_Fezf2_3
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD31136a


title: Astr in vitro, prep X6, Rorb [RNA-Seq]

description:
LAT172A14
X6B_Rorb_3
RNA_deseq_results_TF_OE.csv


title: AB551 input


title: AB551_rep4


title: Astr in vitro, prep X9, EGFP (2) [RNA-Seq]

description:
LAT172A21
X9B_EGFP_4
RNA_deseq_results_TF_OE.csv

value: EGFP

value: Control(EGFP)


title: Breast cancer PD31135a

value: TNBC


title: Astr in vitro, prep X8, EGFP (2) [RNA-Seq]

description:
LAT172A17
X8B_EGFP_3
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD31140a

value: Hypermethylated


title: Breast cancer PD31125a

value: female


title: Astr in vitro, prep X6, EGFP (2) [RNA-Seq]

description:
LAT172A13
X6B_EGFP_3
RNA_deseq_results_TF_OE.csv


title: AB551_rep3

value: breast cancer tissue


title: Breast cancer PD31147a


title: AB551_rep2


title: Breast cancer PD31144a


title: Astr in vitro, prep X9, EGFP [RNA-Seq]

description:
LAT172A10
X9B_EGFP_2
RNA_deseq_results_TF_OE.csv

value: cortical grey matter


title: Astr in vitro, prep X6, BMP 7d, basal 7d [RNA-Seq]

description:
LAT348A1
X6_2D_Bas_2
RNA_deseq_results_maturation_conditions.csv

value: wild type

value: basal medium, 2D culture

value: Control(basal 2D)


title: AB551_rep1

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody


title: Breast cancer PD31107a


title: Breast cancer PD35933a


title: Astr in vitro, prep X8, EGFP [RNA-Seq]

description:
LAT172A5
X8B_EGFP_1
RNA_deseq_results_TF_OE.csv


title: Breast cancer PD31129a


title: Breast cancer PD31130a


title: STG139 rep3

value: Drosophila melanogaster

value: Drosophila S2 cells


title: Breast cancer PD31127a


title: Astr in vitro, prep X6, EGFP [RNA-Seq]

description:
LAT172A2
X6B_EGFP_2
RNA_deseq_results_TF_OE.csv

value: mixed

value: subventricular zone

value: 2 months


title: STG139 rep2


title: Cortical Astr, 2m, prep 3 [RNA-Seq]

description:
LAT597A6
mA10
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

source_name: cortical astrocytes (MACS-purified)

value: cortical astrocytes (MACS-purified)


title: Breast cancer PD31099a


title: Cortical Astr, 2m, prep 2 [RNA-Seq]

description:
LAT597A5
mA7
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv


title: Cortical Astr, 2m, prep 1 [RNA-Seq]

description:
LAT597A4
mA5
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv


title: STG139 rep4


title: Breast cancer PD31112a


title: AB790 rep2


title: STG139 rep1


title: Breast cancer PD31105a


title: Cortical Astr, P4, prep 3 [RNA-Seq]

description:
LAT597A3
iA7
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

value: post natal day 4


title: single cell RNA seq [CE17_I4]

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to Macaca fascicularis reference genome (Macaca_fascicularis_5.0) using TopHat (v 2.0.12) -pass mapping steps.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: UMI_count.txt files include the UMI count values of RefSeq genes

organism: Macaca fascicularis

source_name: Pancreas tissue cells

extract_protocol: Single cell was randomly picked with mouth pipette, then washed by 1mg/ml HSA and transferred into prepared lysis buffer. The cells can store at -80℃ or do it immediately. We used a modified SMART-seq2 protocol to lysis for release all RNA, reverse transcription for capture the cDNA of mRNA and pre-amplification for increase yields of cDNAs. The resulting cDNAs from single cells were barcoded, and then pooled together with different barcode. Followed by 4 cycles, the index of sequence with biotin modified was added at 3’ end.

value: Pancreas

tag: individual

tag: well


title: Breast cancer PD31094a

value: TNBC

value: Hypermethylated


title: Cortical Astr, P4, prep 1 [RNA-Seq]

description:
LAT597A1
iA3
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv


title: AB555M rep2

value: breast cancer tissue


title: Astr in vitro, prep X9 [RNA-Seq]

description:
LAT597A9
X9_B14d_4
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

value: cortical grey matter

value: post natal day 3

value: in vitro differentiated astrocytes


title: Cortical Astr, P4, prep 2 [RNA-Seq]

description:
LAT597A2
iA4
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

value: wild type


title: AB555M rep1

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain


title: single cell RNA seq [CE17_I2]


title: Breast cancer PD31087a

value: female


title: single cell RNA seq [CE17_I3]


title: STG139 input

value: BG4 single-chain antibody

value: Drosophila melanogaster


title: Astr in vitro, prep X8 [RNA-Seq]

description:
LAT597A10
X8_B14d_5
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

value: mixed


title: single cell RNA seq [CE17_I1]


title: Astr in vitro, prep X6 [RNA-Seq]

description:
LAT600A2
X6_B14d_1
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

value: subventricular zone


title: VHIO098_284 rep4

value: Drosophila S2 cells


title: Breast cancer PD31092a


title: Breast cancer PD31093a


title: single cell RNA seq [CE16_I3]


title: VHIO098_284 rep3


title: AB555M rep4


title: AB555M rep3


title: single cell RNA seq [CE16_I4]


title: Breast cancer PD31106a


title: VHIO098_284 rep2


title: Breast cancer PD31068a


title: single cell RNA seq [CE16_I2]


title: VHIO098_284 input


title: single cell RNA seq [CE16_I1]


title: NSC in vitro, prep X9 [RNA-Seq]

description:
LAT597A7
X9_EF_6
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

source_name: cultured neural stem/progenitor cells

value: cultured neural stem/progenitor cells


title: NSC in vitro, prep X6 [RNA-Seq]

description:
LAT600A1
X6_NSC_1
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv

value: 2 months


title: Astr in vitro, prep X9, Lhx2

description:
LAT171A27
B14_Lhx2_R6
ATAC_Deseq_results_TF_OE.csv

data_processing:
Reads from ATAC-Seq fastq files were aligned to the mm10 genome, peaks mapped and quantified using the crickbabs/BABS-ATACSeqPE nextflow pipeline (https://github.com/ crickbabs/BABS-ATACSeqPE; git commit id: 22edccf72855d42e6692a27385cf50666c8f391c).The pipeline was run using nextflow version 0.30.2 (Di Tommaso et al., 2017) with the command “nextflow run main.nf --design ../design.csv --genome mm10 -profile conda --outdir ../results/”.
After initial peak calling, annotation and quantification on the merged dataset, the functional peak annotation and classification was extended using multiple published datasets. First, promoters identified by the original pipeline and peaks overlapping with promoters in the regulatory build of the Ensembl database (version 20161111), were classified as “promoters". Other peaks were classified as putative enhancers, if they were overlapping with enhancers it the Ensembl regulatory build, or if they were overlapping with peaks of the enhancer mark H3K4me1 in forebrain P0 or adult cortex in published datasets from the Encode database (https://www.encodeproject.org/; bed files, datasets ENCFF172LKQ, ENCFF746YEV). As a quality control, the ATAC-Seq peaks were also overlapped with DNase-Seq peaks from E18.5 and adult brain (bed files, Encode datasets ENCFF591XUM, ENCFF865BUI).
To identify potential regulatory interactions, the original pipeline annotated each peak to the closest TSS. To include potential long-range interactions, distal peaks (i.e. peaks not classified as promoters) were annotated to additional genes, if the peaks were overlapping with regulatory regions for these genes in brain E14.5 or adult cortex described by Shen et al. (Shen et al., 2012), or regulatory regions in adult cortex or cultured neural progenitors (data for confidence level p <0.01) described by Ron et al. (Ron et al., 2017). The conversion of mm9 genome coordinates to mm10 coordinates for these datasets was performed with the Ensembl Assembly Converter (https://www.ensembl.org/Homo_sapiens/Tools/ AssemblyConverter?db=core).
Normalisation of read counts and analysis of differential accessibility for the peak regions called on the merged dataset was performed using the Bioconductor “DESeq2” package.
Genome_build: mm10
Supplementary_files_format_and_content: Peak coordinates, peak type and putative target gene; read counts for each peak; DESeq2 results: normalised expression and statistics; cortical in vivo samples included;

extract_protocol:
ATAC sequencing libraries were prepared using the OMNI-ATAC protocol (Corces et al., 2017) with minor modifications. 25,000 MACS-purified astrocytes or dissociated cultured cells were collected by centrifugation (300g, 5 min, 4C), and permeabilized for 3 min on ice in 50 ul ATAC-RSB buffer (Tris/HCl (pH7.4) 10 mM, NaCl 10 mM, MgCl2 3 mM) containing 0.1 % NP-40 (IGEPAL CA-630), 0.1% Tween-20 and 0.01% digitonin. 1 ml ATAC-RSB buffer containing 0.1 % Tween-20 was added and the nuclei were recovered by centrifugation (500g, 10 min, 4C). The pellet was resuspended in 25 ul of transposase reaction mix (12.5 ul 2x TD buffer and 1.25 ul Tn5 transposase (Illumina Cat #FC-121-1030), 8.25 ul PBS, 2.5 ul water, 0.1% Tween-20, 0.01% digitonin), and incubated on a rotational shaker (1000 rpm) for 30 min at 37C to fragment and tag accessible chromatin. DNA was then purified using the “MinElute PCR purification kit” (Qiagen, Cat no. 28004) and eluted in 20 ul EB buffer (Qiagen).
5 ul DNA were were amplified by PCR in 20 ul reactions using NEBNext HiFi 2x PCR Master Mix (New England Biolabs, M0541) and barcoded primers described previously (Buenrostro et al., 2013) for 12 cycles: (1) 5 min 72C, (2) 30s 98C, (3) repeat 12x: 10s 98C, 30s 63C, 60s 72C. The amplified libraries were purified using SPRIselect beads (ratio sample : beads 1 : 1.8)


title: Astr in vitro, prep X8, Lhx2

description:
LAT171A22
B14_Lhx2_R5
ATAC_Deseq_results_TF_OE.csv


title: VHIO098_181 rep4


title: AB555M input


title: VHIO098_284 rep1


title: VHIO098_181 rep3


title: VHIO098_181 rep2


title: NSC in vitro, prep X8 [RNA-Seq]

description:
LAT597A8
X8_EF_5
RNA_deseq_results_in_vivo_vs_in_vivo_baseline.csv


title: Breast cancer PD31059a


title: Breast cancer PD31067a


title: single cell RNA seq [CE15_I4]

value: Pancreas


title: VHIO098_181 rep1


title: single cell RNA seq [CE14_I4]


title: VHIO098_181 input


title: single cell RNA seq [CE14_I3]


title: Astr in vitro, prep X9, Dbx2, run 1

description:
LAT171A11
B14_Dbx2_R3
ATAC_Deseq_results_TF_OE.csv


title: Astr in vitro, prep X9, Dbx2, run 2


title: Astr in vitro, prep X8, Dbx2, run 1

description:
LAT171A8
B14_Dbx2_R2
ATAC_Deseq_results_TF_OE.csv


title: HCI009 rep4


title: Astr in vitro, prep X8, Dbx2, run 2


title: single cell RNA seq [CE14_I2]


title: Astr in vitro, prep X6, Dbx2, run 2

description:
LAT171A4
B14_Dbx2_R1
ATAC_Deseq_results_TF_OE.csv


title: Astr in vitro, prep X6, Dbx2, run 1


title: HCI009 rep3


title: Breast cancer PD31061a

value: TNBC


title: Breast cancer PD31051a


title: HCI009 rep1


title: Astr in vitro, prep X9, Rorb

description:
LAT171A24
B14_Rorb_R6
ATAC_Deseq_results_TF_OE.csv

value: Rorb


title: single cell RNA seq [CE14_I1]


title: HCI009 rep2

value: breast cancer tissue


title: single cell RNA seq [CE13_I3]


title: single cell RNA seq [CE13_I4]


title: single cell RNA seq [CE13_I2]


title: HCI009 input


title: AB863M rep4


title: AB863M rep3


title: single cell RNA seq [CE12_I3]


title: single cell RNA seq [CE12_I4]


title: AB863M rep2


title: AB863M rep1


title: Astr in vitro, prep X9, EGFP,  exp2

description:
LAT171A23
B14_EGFP_R6
ATAC_Deseq_results_TF_OE.csv

value: cortical grey matter

value: EGFP

value: Control(EGFP)


title: single cell RNA seq [CE12_I2]


title: Tumourspheres from MB3W1 cell line

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

description:
Read1: Unique Molecular Index
Read2: mRNA sequence tag

data_processing:
Fastq files prepared using 10X CellRanger mkfastq software (v3.0.2)
Cells counted and feature-barcode matrices generated using 10X Cellranger count software (v3.0.2) using the GRCh38-3.0.0 reference provided by 10X Genomics, and a targeted cell count of 5,000
Genome_build: GRCh38
Supplementary_files_format_and_content: 10x filtered feature-barcode matrices

source_name: Dietl et al., BMC Cancer 2016

growth_protocol: Tumorspheres were grown in StemPro NSC Serum-Free Medium (HDMB03), Neural Precursor media (D283) and Stem Cell media (MB3W1) on ultra-low attachment tissue culture plates

extract_protocol: Single-cell cDNA libraries were generated using 10x Genomics Single Cell 3' Reagents Kits v3 and Chromium controller

treatment_protocol: 6000 HDMB03, MB3W1 and D283 cells were dissociated to single cell suspension for single-cell cDNA generation and analysis

value: Tumorspheres from Group 3 medulloblastoma cell line

tag: cell line


title: Breast cancer PD31049a

value: Hypermethylated


title: Breast cancer PD31043a

value: female


title: Tumourspheres from HDMB03 cell line

source_name: T Milde et al., J Neurooncol 2012


title: Astr in vitro, prep X8, EGFP, run 1

description:
LAT171A5
B14_EGFP_R2
ATAC_Deseq_results_TF_OE.csv

value: post natal day 3

value: in vitro differentiated astrocytes


title: single cell RNA seq [CE11_I4]


title: AB521M rep2

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody

value: Drosophila melanogaster


title: Astr in vitro, prep X8, Rorb

description:
LAT171A19
B14_Rorb_R5
ATAC_Deseq_results_TF_OE.csv

value: mixed


title: AB521M rep1

value: Drosophila S2 cells


title: Astr in vitro, prep X6, Rorb

description:
LAT171A15
B14_Rorb_R4
ATAC_Deseq_results_TF_OE.csv

value: subventricular zone

value: 2 months


title: single cell RNA seq [CE11_I2]

value: Pancreas


title: Tumourspheres from D283 cell line

source_name: Friedman et al., J Neuropathol Exp Neurol 1985


title: Astr in vitro, prep X6, Lhx2

description:
LAT171A17
B14_Lhx2_R4
ATAC_Deseq_results_TF_OE.csv


title: Breast cancer PD31044a

value: TNBC


title: Astr in vitro, prep X9, EGFP, run 2

description:
LAT171A9
B14_EGFP_R3
ATAC_Deseq_results_TF_OE.csv

value: cortical grey matter


title: AB863M input

value: breast cancer tissue


title: PAX6-GOFN1_S9_R1.fastq.gz

data_processing:
quantification of GENCODE v27 transcripts using salmon v. 0.9.1
fold change analsyis using DESeq2 as follows
Quantification data read using the tximport library
DESeqDataSet constructed with all nine libraries from three conditions. Analysis using the model '~condition'
Fold changes calculated between control and each GOF treatment using the lfcShrink() function with the 'apeglm' method.
Genome_build: GRCh38
Supplementary_files_format_and_content: fold change and transcript quantification files

source_name: HDMB03 (T Milde et al., J Neurooncol 2012)

growth_protocol: Tumorspheres were grown in StemPro NSC Serum-Free Medium (Life Technologies) on ultra-low attachment tissue culture plates

extract_protocol:
Whole RNA was extracted from PAX GOF tumorspheres using the Norgen RNA extraction kit (Norgen Biotek)
Illumina TruSeq RNA v2 kit (unstranded)

treatment_protocol: PAX GOF tumorsphere were generated by lentiviral transduction at MOI =0.3 as per Dharmacon lentiviral transduction protocols

tag: condition

value: PAX6 gain of function

tag: treatment

value: Transduced with PAX6 ORF lentivirus

value: Tumourspheres from group 3 medulloblastoma cell line


title: Astr in vitro, prep X6, EGFP, exp2

description:
LAT171A13
B14_EGFP_R4
ATAC_Deseq_results_TF_OE.csv

value: EGFP

value: Control(EGFP)


title: Astr in vitro, prep X6, EGFP, run 2

description:
LAT171A2
B14_EGFP_R1
ATAC_Deseq_results_TF_OE.csv

value: in vitro differentiated astrocytes


title: single cell RNA seq [CE11_I3]


title: Astr in vitro, prep X6, EGFP, run 1


title: single cell RNA seq [CE11_I1]


title: PAX3-GOFN5_S3_R1.fastq.gz

value: PAX3 gain of function

value: Transduced with PAX3 ORF lentivirus


title: Breast cancer PD31029a

value: Hypermethylated

value: female


title: Astr in vitro, prep X8, EGFP, run 2

value: mixed

value: post natal day 3


title: AB521M rep3

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

tag: chip antibody

value: BG4 single-chain antibody

tag: spike-in reference organsms

value: Drosophila melanogaster

value: Drosophila S2 cells


title: AB521M input

value: breast cancer tissue

tag: strain

tag: spike-in cell line


title: HCI005 rep4


title: single cell RNA seq [CE15_I3]

tag: tissue

value: Pancreas


title: Astr in vitro, prep X9, 3D, BMP 7d, FGF2 7d

description:
LAT349A12
FGF_3D_R3
ATAC_Deseq_results_maturation_conditions.csv

value: cortical grey matter

tag: age

tag: genotype

value: wild type

value: FGF medium, 3D culture


title: single cell RNA seq [CE10_I3]


title: PAX3-GOFN4_S5_R1.fastq.gz

value: Tumourspheres from group 3 medulloblastoma cell line


title: HCI005 rep3

tag: cell type


title: single cell RNA seq [CE15_I1]


title: Astr in vitro, prep X8, 3D, BMP 7d, FGF2 7d

description:
LAT349A8
FGF_3D_R2
ATAC_Deseq_results_maturation_conditions.csv

value: in vitro differentiated astrocytes


title: single cell RNA seq [CE10_I2]


title: PAX3-GOFN1_S1_R1.fastq.gz

value: PAX3 gain of function


title: HCI005 rep2


title: Astr in vitro, prep X6, 3D, BMP 7d, FGF2 7d

description:
LAT349A4
FGF_3D_R1
ATAC_Deseq_results_maturation_conditions.csv

value: subventricular zone

value: 2 months


title: ControlN4_S4_R1.fastq.gz

description:
PAX3_GOF_all_salmon.txt
PAX6_GOF_all_salmon.txt

value: control

value: Transduced with RFP control lentivirus


title: single cell RNA seq [CE13_I1]


title: single cell RNA seq [CE12_I1]


title: HCI005 rep1


title: single cell RNA seq [CE10_I1]


title: ControlN3_S6_R1.fastq.gz


title: Astr in vitro, prep X9, 3D, BMP 7d, basal 7d

description:
LAT349A11
bas_3D_R3
ATAC_Deseq_results_maturation_conditions.csv

value: mixed

value: post natal day 3

value: basal medium, 3D culture


title: AB521M rep4

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody

value: Drosophila melanogaster


title: HCI005 input

value: breast cancer tissue

value: Drosophila S2 cells


title: single cell RNA seq [CE09_I4]

value: Pancreas


title: Astr in vitro, prep X9, EGFP, run 1

value: cortical grey matter

value: EGFP

value: Control(EGFP)


title: Astr in vitro, prep X8, 3D, BMP 7d, basal 7d

description:
LAT349A7
bas_3D_R2
ATAC_Deseq_results_maturation_conditions.csv

value: wild type

value: in vitro differentiated astrocytes


title: ControlN1_S7_R1.fastq.gz

value: Tumourspheres from group 3 medulloblastoma cell line


title: Astr in vitro, prep X6, 3D, BMP 7d, basal 7d

description:
LAT349A3
bas_3D_R1
ATAC_Deseq_results_maturation_conditions.csv

value: subventricular zone

value: 2 months


title: OTX2high

data_processing:
trimming with trimmmomatic 0.36
Alignment to GRCh38 using bowtie 2.3.3.1
Peak calling using MACS 2.1.1.20160309
Genome_build: GRCh38
Supplementary_files_format_and_content: BAM alignment files and MACS peak files

source_name: American Type Culture Collection

growth_protocol: D283 tumorspheres were grown on ultra-low attachment plates in Neural Precursor media (DMEM/F12, B27 supplement (1X), N2 supplement (1X), hbFGF (20ng/mL), hEGF (20ng/mL)) following OTX2 silencing.

extract_protocol:
The reaction was then quenched with 0.125 M Glycine for 10 minutes. Cells were washed twice with 1X PBS. Chromatin was mechanically sheered in sonication buffer (HEPES pH 7.9 (50 mM), NaCl (140 mM, EDTA (1 mM), Triton (1%), Na-deoxycholate (0.1%), SDS (1%), PIC (1X)). Immunoprecipitation was carried out with H3K27me3 (07-449, Millipore) and H3K4me3 (07-473, Millipore) antibodies overnight at 4°C. Antibody complexes were captured on Dynabeads (Invitrogen) for 4 hours at 4°C then washed with Low Salt buffer (SDS (0.1%), Triton (1%), EDTA (2mM), Tris-HCl pH 8.1 (20 mM), NaCl (150 mM)), High Salt buffer (SDS (0.1%), Triton (1%), EDTA (2mM), Tris-HCl pH 8.1 (20 mM), NaCl (500 mM)), LiCl buffer (LiCl (0.25M), Na-deoxycholate (1%), EDTA (1mM), Tris-HCl pH 8.1 (10mM), NP-40 (1%)) and TE. Antibody complexes were eluted from the beads and reverse cross-linked for 12-16 hours at 65°C. Chromatin was then incubated in RNase A (0.2mg/mL) and NaCl (0.2 M/mL) for 2 hours. Proteinase K (0.2 mg/mL) was then added for an additional 2 hours. Chromatin was then cleaned using the Qiagen PCR Purification Kit according to manufacturer’s instructions.
NextFlex Illumina Chip-seq kit

treatment_protocol: OTX2 silencing was performed on D283 cells using 30 nM Silencer select siRNA (Life Technologies). Non-silencing Scramble siRNA were used as a negative control.

tag: antibody

value: IgG control

tag: otx2 silencing


title: single cell RNA seq [CE09_I2]


title: OTX2low


title: Astr in vitro, prep X9, BMP 7d, FGF2 7d

description:
LAT349A10
FGF_2D_R3
ATAC_Deseq_results_maturation_conditions.csv

value: mixed

value: post natal day 3

value: FGF medium, 2D culture

tag: experimental group

value: FGF


title: single cell RNA seq [CE09_I1]


title: STG331 rep4

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody

value: Drosophila melanogaster


title: H3K27me3OTX2low

value: H3K27me3 antibody


title: STG331 rep3

value: breast cancer tissue

value: Drosophila S2 cells


title: single cell RNA seq [CE08_I4]

value: Pancreas


title: STG331 rep2


title: Astr in vitro, prep X8, BMP 7d, FGF2 7d

description:
LAT349A6
FGF_2D_R2
ATAC_Deseq_results_maturation_conditions.csv

value: cortical grey matter

value: wild type


title: Astr in vitro, prep X6, BMP 7d, FGF2 7d

description:
LAT349A2
FGF_2D_R1
ATAC_Deseq_results_maturation_conditions.csv

value: in vitro differentiated astrocytes


title: H3K27me3OTX2high


title: STG331 rep1


title: H3K4me3OTX2low

value: H3K4me3 antibody


title: single cell RNA seq [CE08_I2]


title: single cell RNA seq [CE09_I3]


title: Astr in vitro, prep X8, BMP 7d, basal 7d

description:
LAT349A5
bas_2D_R2
ATAC_Deseq_results_maturation_conditions.csv

value: basal medium, 2D culture

value: Control(basal 2D)


title: Astr in vitro, prep X9, BMP 7d, basal 7d

description:
LAT349A9
bas_2D_R3
ATAC_Deseq_results_maturation_conditions.csv

value: mixed


title: single cell RNA seq [CE08_I1]


title: H3K4me3OTX2high


title: single cell RNA seq [CE07_I4]


title: D2_B: Double deficiency replicate 2

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

institute: Centre for Research in Agrigenomics

data_processing:
Illumina sequencing reads were generated using HiSeq 2500 platform by Novogene (Beijing, China)
Reads were treated with Trimmomatic to remove adapter sequences, aligned to the Araport11 genome reference with Tophat 2.1.1 and the counts and differential expression files generated with Cufflinks/Cuffdiff.
Genome_build: Araport11
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample according to Cufflinks

organism: Arabidopsis thaliana

source_name: Rossete leafs

growth_protocol: Arabidopsis plants were grown on soil for 12 d before been transferred to hydroponic systems and cultivated for 10 d under 1/10 Hoagland as in Hermans and Verbruggen (2005; J Exp Botany) with modifications for copper (CuSO4 1 µM). Long day conditions (diurnal phase: 22 h; 23°C; 120 µmols m-2 s-1 and night phase: 8 h; 18°C) were applied and all samples were harvested 4 h after the light onset.

extract_protocol:
Rosette leaves were flash frozen in liquid nitrogen and total RNA prepared using Trizol according to the manufacturer's instructions.
RNA libraries were prepared by Novogene (Beijing, China) for sequencing using standard Illumina protocols (HiSeq 2500 platform).
RNA-Seq for First Read unstranded libraries

treatment_protocol: After 10 d of adaptation, plants were kept under the same (control) conditions or under copper deficiency  (no CuSO4 and Bathocuproinedisulfonic acid disodium salt 10 µM), iron deficiency (no FeEDTA) or both deficiencies for 10 additional days.

tag: ecotype

tag: Stage

value: 20-d-old plants

tag: treatment lenght

value: rosette leaves


title: single cell RNA seq [CE08_I3]

tag: individual

tag: well


title: Astr in vitro, prep X6, BMP 7d, basal 7d

description:
LAT349A1
bas_2D_R1
ATAC_Deseq_results_maturation_conditions.csv

value: subventricular zone

value: 2 months

tag: treatment


title: Cortical Astr, 2m, prep 4, run 2

description:
LAT596A7
Astr_ad_R4
ATAC_Deseq_results_in_vivo_only.csv

value: cortical astrocytes (MACS-purified)


title: PAX6-GOFN2_S2_R1.fastq.gz

tag: condition

value: PAX6 gain of function

value: Transduced with PAX6 ORF lentivirus

value: Tumourspheres from group 3 medulloblastoma cell line


title: STG331 input

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

tag: chip antibody

value: BG4 single-chain antibody

tag: spike-in reference organsms

value: Drosophila melanogaster

value: Drosophila S2 cells


title: STG316 rep1

tag: strain

tag: spike-in cell line


title: D2_A: Double deficiency replicate 1

tag: tissue


title: Astr in vitro, prep X8, EGFP,  exp2

description:
LAT171A18
B14_EGFP_R5
ATAC_Deseq_results_TF_OE.csv

value: cortical grey matter

tag: age

value: post natal day 3

tag: genotype

value: EGFP

value: in vitro differentiated astrocytes

value: Control(EGFP)


title: single cell RNA seq [CE07_I2]

value: Pancreas


title: STG316 input

tag: cell type


title: STG316 rep4


title: Cortical Astr, 2m, prep 4, run 1

value: wild type


title: F2_B: Iron deficiency replicate 2

value: 20-d-old plants

value: rosette leaves


title: F2_A: Iron deficiency replicate 1


title: AB580 input


title: Cortical Astr, 2m, prep 3, run 1

description:
LAT596A6
Astr_ad_R3
ATAC_Deseq_results_in_vivo_only.csv

value: 2 months

value: cortical astrocytes (MACS-purified)


title: single cell RNA seq [CE06_I4]


title: single cell RNA seq [CE07_I1]


title: C2_C: Copper deficiency replicate 2


title: Cortical Astr, 2m, prep 2, run 2

description:
LAT596A2
Astr_ad_R2
ATAC_Deseq_results_in_vivo_only.csv


title: single cell RNA seq [CE15_I2]


title: STG316 rep2


title: single cell RNA seq [CE07_I3]


title: single cell RNA seq [CE06_I3]


title: C2_B: Copper deficiency replicate 1


title: STG201_284 rep3


title: Cortical Astr, 2m, prep 2, run 1


title: Cortical Astr, 2m, prep 3, run 2


title: single cell RNA seq [CE06_I2]


title: STG201_284 rep4


title: Cortical Astr, 2m, prep 1, run 2

description:
LAT596A1
Astr_ad_R1
ATAC_Deseq_results_in_vivo_only.csv


title: STG201_284 rep2


title: K2_A: Control replicate 1


title: PAX6-GOFN3_S8_R1.fastq.gz

value: PAX6 gain of function

value: Transduced with PAX6 ORF lentivirus

value: Tumourspheres from group 3 medulloblastoma cell line


title: STG201_284 rep1

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody


title: Cortical Astr, 2m, prep 1, run 1

value: cortical grey matter


title: STG201_284 input

value: Drosophila melanogaster

value: Drosophila S2 cells


title: single cell RNA seq [CE05_I3]


title: Cortical Astr, P4, prep 3, run 2

description:
LAT596A5
Astr_P4_R3
ATAC_Deseq_results_in_vivo_only.csv

value: post natal day 4


title: K3 FCR d3

city: Munich

first: Thomas

last: Carell

state: Bavaria

address: Butenandtstr. 5-13

department: Chemistry

country: Germany

institute: Ludwig Maximilian University Munich

description:
Sample 3
bisulfite treated
Extracted_sDMRs_CF1_K3.txt
sDMRs.bed

data_processing:
basecalls were directly obtained through the Illumina MiSeq software
Sequenced reads were trimmed for adaptor sequence and masked for low-quality sequence using TrimGalore version 0.5.0, Cutadapt version 1.17, in paired-end trimming mode with parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA (R1)/AGATCGGAAGAGC (R2)
Trimmed reads were mapped to imprint-containing, bisulfite converted chromosomes 2, 7, 11,12 and 17 from mm10 using bsmap v2.90 with parameters -v 5 -p 3 -I 8 -n 1 -r 0
Methylation ratios were extracted from .sam files using a custom Python script to generate a matrix table
Genome_build: mm10
Supplementary_files_format_and_content: Extracted_sDMRs_CF1_K3.txt:  matrix text file tabulates methylation ratios at selected somatic imprint regions (Column headers/seven locus identifiers (x_S# format):  The part before the underscore corresponds to the official gene symbol, while letter and number after the underscore identify the amplicon design.  Each of the headers/seven locus identifiers appears four times as the columns report the methylation ratios for the four biological samples analyzed. The first seven columns correspond to sample 1, the next seven columns to sample 2 and so on.)
sDMRs.bed:  bed file with genomic coordinates of target loci

source_name: embryonic stem cells

growth_protocol: mouse embryonic stem cells were either cultured in alterantive naïve/formative-like state using basal medium containing 10% FBS supplemented with Src inhibitor CGP77675, Gsk3 inhibitor CHIR99021 and Leukemia Ihibitory Factor (alternative two inhibitors and LIF, alias a2iL; sample 2) or transited to primed state by culture in the same basal medium supplemented with Tankyrase inhibitor IWR1 and CHIR99021 (FCR) for three (sample 3) or five days (sample 4)

extract_protocol:
genomic DNA was isolated silica-based spin columns as described in Traube et al. (Nat. Protocols 14:283) and bisulfite treated with EpiTect Bisulfite Kit (Qiagen 59104) as described in Spada et al. (https://www.biorxiv.org/content/10.1101/846584v2)
bisulfite treated genomic DNA was first amplifiied using target-specific primers with 5'-overhangs followed by a second amplification round with overhang-specific, Illumina-compatible indexing primers as described in Mullholand et al. (https://doi.org/10.1101/321604) and Spada et al. (https://www.biorxiv.org/content/10.1101/846584v2).
multiplexed targeted amplicon sequencing

value: embryonic stem cells

tag: culture conditions

value: IWR1-endo, CHIR99021, LIF; 3 days


title: K3 FCR d5

description:
Sample 4
bisulfite treated
Extracted_sDMRs_CF1_K3.txt
sDMRs.bed

value: wild type

value: IWR1-endo, CHIR99021, LIF; 5 days


title: Cortical Astr, P4, prep 3, run 1

tag: experimental group


title: STG201_181 rep4


title: K3 Fa2iL

description:
Sample 2
bisulfite treated
Extracted_sDMRs_CF1_K3.txt
sDMRs.bed


title: Cortical Astr, P4, prep 2, run 2

description:
LAT596A4
Astr_P4_R2
ATAC_Deseq_results_in_vivo_only.csv


title: single cell RNA seq [CE05_I2]

value: Pancreas


title: single cell RNA seq [CE05_I1]


title: K2_B: Control replicate 2

tag: ecotype

value: 20-d-old plants

value: rosette leaves


title: CF-1 mEFs

description:
Sample 1
bisulfite treated
Extracted_sDMRs_CF1_K3.txt
sDMRs.bed

source_name: primary embryonic fibroblasts

value: primary embryonic fibroblasts

value: standard


title: Cortical Astr, P4, prep 2, run 1

value: cortical astrocytes (MACS-purified)


title: single cell RNA seq [CE04_I4]


title: single cell RNA seq [CE06_I1]


title: STG201_181 rep2

value: breast cancer tissue


title: SUM159_GR_ChIP-seq

city: Salt Lake City

first: Katherine

middle: E

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

data_processing:
Fastq files from ChIP-seq were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t –best -q -S -l 32 -e 80 -n 2.
ChIP-seq peaks were identified by using Model-Based Analysis of ChIP-seq-2 (MACS2)  with a p value cutoff of 1e -10 and the mfold parameter constrained between 15 and 100.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table of read counts in peak regions in each sample

source_name: SUM159 Cell Line

growth_protocol: The following cell lines: MDA-MB-231, MDA-MB-361 , MDA-MB-453, were cultured in DMEM media (Gibco, ThermoFisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (Hyclone, GE Healthcare, Logan, UT), 1 mM sodium pyruvate, and non-essential amino acids (Gibco). HCC70, HCC1187, HCC1937  were cultured in RPMI media (Gibco), supplemented with 10% fetal bovine serum (Hyclone), 10 mM HEPES (Sigma-Aldrich, St. Louis, MO), 1 mM sodium pyruvate (Gibco), and 4.5 g/l glucose (Sigma-Aldrich). BT474 were cultured in RPMI, 10% fetal bovine serum, 10 mM HEPES, 1mM sodium pyruvate, 4.5g/l glucose, 10µg/ml insulin. MCF-7 cells were cultured in EMEM, 10% fetal bovine serum, 1mM sodium pyruvate, non-essential amino acids and 10µg/ml insulin. SUM159 cells were cultured in Ham’s F12, 5% fetal bovine serum, 1µg/ml hydrocortisone, and 5µg/ml insulin. Cells were passaged and harvested at 80% confluence.

extract_protocol:
For ChIP experiments, protein-DNA complexes were covalently cross-linked by incubating cells in 1% formaldehyde for 10 min at room temperature. Cells were incubated with 0.125 M glycine for 5 min, to quench cross-linking reaction. Cells were washed and scraped with PBS (pH 7.4) (Lonza). Cells were lysed with Farnham Lysis Buffer (5mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) containing protease inhibitor (Roche). Cell lysate was centrifuged at 2,000 rpm for 5 min at 4 °C. The crude nuclear extract contained in the supernatant was stored at −80 °C.
ChIP-seq libraries were constructed as described  here: https://www.encodeproject.org/documents/df9dd0ec-c1cf-4391-a745-a933ab1af7a7/@@download/attachment/Myers_Lab_ChIP-seq_Protocol_v042211.pdf

value: 100nM dexamethasone

tag: cell line


title: single cell RNA seq [CE04_I3]


title: MDA-MB-453_GR_ChIP-seq

source_name: MDA-MB-453 Cell Line


title: Cortical Astr, P4, prep 1, run 2

description:
LAT596A3
Astr_P4_R1
ATAC_Deseq_results_in_vivo_only.csv


title: Cortical Astr, P4, prep 1, run 1


title: STG201_181 input

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody


title: single cell RNA seq [CE04_I2]


title: MDA-MB-361_GR_ChIP-seq

source_name: MDA-MB-361 Cell Line


title: Astr in vitro, prep X8

description:
LAT596A13
Astr_in_vitro_R3
ATAC_Deseq_results_in_vivo_vs_in_vitro_baseline.csv

source_name: in vitro differentiated astrocytes

value: mixed

value: cortical grey matter

value: post natal day 3

value: in vitro differentiated astrocytes

value: Astr_BMP (Astr_B14)


title: single cell RNA seq [CE04_I1]


title: STG201_181 rep3

value: Drosophila melanogaster

value: Drosophila S2 cells


title: AB580 rep4


title: MDA-MB-231_GR_ChIP-seq

source_name: MDA-MB-231 Cell Line


title: Astr in vitro, prep X6

description:
LAT596A12
Astr_in_vitro_R2
ATAC_Deseq_results_in_vivo_vs_in_vitro_baseline.csv

value: subventricular zone

value: 2 months

value: wild type


title: AB580 rep3

source_name: fixed human breast cancer PDTX tissue


title: single cell RNA seq [CE03_I4]

value: Pancreas


title: Astr in vitro, prep X9

description:
LAT596A11
Astr_in_vitro_R1
ATAC_Deseq_results_in_vivo_vs_in_vitro_baseline.csv


title: single cell RNA seq [CE03_I3]


title: AB580 rep2


title: HCC70_GR_ChIP-seq

source_name: HCC70 Cell Line


title: NSC in vitro, prep X8

description:
LAT596A9
NSC_in_vitro_R3
ATAC_Deseq_results_in_vivo_vs_in_vitro_baseline.csv


title: STG201_181 rep1


title: AB580 rep1


title: single cell RNA seq [CE03_I2]

source_name: Pancreas tissue cells


title: single cell RNA seq [CE03_I1]


title: NSC in vitro, prep X6

description:
LAT596A8
NSC_in_vitro_R2
ATAC_Deseq_results_in_vivo_vs_in_vitro_baseline.csv


title: HCC1187 _GR_ChIP-seq

source_name: HCC1187 Cell Line


title: PAR1022 input


title: single cell RNA seq [CE01_I4]


title: PAR1022 rep4


title: PAR1022 rep3


title: single cell RNA seq [CE01_I3]


title: SUM159_STAT3_ChIP-seq

value: EtOH


title: BT474_GR_ChIP-seq

source_name: BT474 Cell Line


title: NSC in vitro, prep X9

description:
LAT596A10
NSC_in_vitro_R1
ATAC_Deseq_results_in_vivo_vs_in_vitro_baseline.csv


title: single cell RNA seq [CE01_I2]


title: MCF-7_GR_ChIP-seq

source_name: MCF-7 Cell Line


title: PAR1022 rep2


title: single cell RNA seq [CE10_I4]


title: MDA-MB-453_STAT3_ChIP-seq


title: PAR1022 rep1


title: BTnc035 complement rep1

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Basecalling: Illumina version 2.2.0
Read trimming: Cutadapt version 2.5 including –nextseq-trim=20 switch to handle two-color sequencing.
Reads were mapped to the B. thetaiotaomicron VPI-5482 genome and plasmid using the READemption pipeline that employs the Segemehl algorithm for split reads.
Genome_build: NC_004663.1 (chromosome), NC_004703.1 (plasmid)

organism: Bacteroides thetaiotaomicron

source_name: cultures

growth_protocol: Samples 1-18: Wild-type B. thetaiotaomicron VPI-5482 was grown overnight in 5 mL pre-reduced TYG medium followed by sub-culturing (1:100) into 100 mL fresh pre-reduced TYG. Total RNA was extracted from culture aliquots of three biological replicates at early-exponential (4 h), mid-exponential (7 h), and stationary growth phases (10 h). Samples 19-24: B. thetaiotaomicron wild-type  (tdk mutant background),  ∆BTnc035, (BTnc035 deletion mutant), and BTnc035+ (BTnc035 complementation strain) strains were grown in TYG to stationary phase, followed by the addition of anhydrotetracycline at a final concentration of 200 ng/mL, and resumed growth therein for 2 h.

extract_protocol:
Total RNA was isolated by hot phenol extraction from 4 OD equivalents of culture to which 1.6 mL stop mix (Eriksson et al., 2003) was added (95% v/v ethanol, 5% v/v water saturated phenol, pH >7.0). The cells were lysed by incubation with 600 μL lysozyme (0.5 mg/mL) and 60 μL 10% SDS for 2 min at 64°C, followed by the addition of 66 μL 3 M NaOAc. Phenol extraction (750 μL; Roti-Aqua phenol) was performed at 64°C for 6 min with the subsequent addition of 750 µL of chloroform. RNA was precipitated from the aqueous phase with twice the volume of 30:1 (ethanol : 3 M NaOAc, pH 6.5) mix and incubated at –80°C overnight. After centrifugation, pellets were washed with 75% (vol/vol) ethanol and re-suspended in 50 μL H2O. Contaminating genomic DNA was removed by treating 40 μg total RNA with 5 U of DNase I (Fermentas) and 0.5 μL Superase-In RNase Inhibitor (Ambion) in a 50 μL reaction (1 U/µL, Fermentas). RNA quality was checked using a 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies). RNA integrity (RIN) values for all samples were >7.
Samples 1-18: Prior to cDNA synthesis, total RNA was fragmented using ultrasound (4 pulses of 30 sec at 4°C) and treated with T4 Polynucleotide Kinase. Subsequently, half the total RNA of each sample was treated with Terminator exonuclease (TEX) to enrich for primary transcripts. RNA samples were then poly (A)-tailed using poly (A) polymerase and 5’-PPP was removed with 5’ Polyphosphatase. RNA adaptors were ligated and first-strand cDNA synthesis was carried out using oligo (dT) primers and M-MLV reverse transcriptase. The cDNA was PCR amplified to about 10-20 ng/μL, purified using Agencourt AMPure XP kit and fractionated in a size range of 200-500 bp. Samples 19-24: cDNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep kit for Illumina in accordance with the manufacturers’ instructions with modifications: RNA samples were fragmented with Mg2+ at 94˚C for 2.75 min using the NEBNext Magnesium RNA Fragmentation Module followed by RNA purification with the Zymo RNA Clean & Concentrator kit. Fragmented RNA was dephosphorylated at the 3’ end, phosphorylated at the 5’ end and decapped using 10 U T4-PNK +/- 40 nmol ATP and 5 U RppH, respectively. After each enzymatic treatment, RNA was purified with the Zymo RNA Clean & Concentrator kit. The small RNA fragments were ligated for cDNA synthesis to 3’ SR adapter and 5’ SR adapter diluted 1:3 with nuclease-free water before use. PCR amplification to add Illumina adaptors and indices to the cDNA was performed for 14 cycles with 1:3 diluted primer. Barcoded DNA libraries were purified using magnetic MagSi-NGSPREP Plus beads at a 1.8 ratio of beads to sample volume.
Samples 1-18: dRNA-seq; samples 19-24: RNA-seq


title: single cell RNA seq [CE01_I1]


title: MDA-MB-361_STAT3_ChIP-seq


title: VHIO179_284 rep4


title: HCC1937_GR_ChIP-seq

source_name: HCC1937 Cell Line


title: MDA-MB-231_STAT3_ChIP-seq


title: BTnc035 KO rep1


title: DHT PDX HCI-009 3942

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

description: DHT 4

data_processing:
Reads generated were mapped to the human genome (GRCH38) by gSNAP (CITE2)
Expression (FPKM) derived by Cufflinks (CITE2)
Differential expression analyzed with ANOVA in R.

source_name: Patient derived xenograft tumors

growth_protocol: PDX tumors were propogated in the mammary glands of  NOD/SCID/gamma mice

extract_protocol:
mRNA was extracted from frozen tissue using TRIzol and was Bioanalyzed prior to sequencing
RNA libraries were prepared used Illumina HiSeq libraries according to manufacturer’s instructions for the TruSeq Stranded RNA kit

treatment_protocol: Mice were implanted with cellulose control or slow release 8mg DHT pellets prior to tumor implantation. Tumor tissue was collect 9 weeks later.

tag: pdx

value: HCI-009 TNBC

tag: mouse strain

value: NOD scid gamma

value: Hormone:Slow release 8mg DHT pellet, 9wk


title: MCF7_STAT3_ChIP-seq

source_name: MCF7 Cell Line


title: single cell RNA seq [CE05_I4]

tag: individual

tag: well


title: VHIO179_284 rep3

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain


title: DHT PDX HCI-009 3941

description: DHT 3

tag: treatment


title: VHIO179_284 rep2

tag: chip antibody

value: BG4 single-chain antibody


title: BTnc035 complement rep2


title: DHT PDX HCI-009 3940

description: DHT 2


title: HCC70_STAT3_ChIP-seq


title: HCC1937_STAT3_ChIP-seq


title: BTnc035 KO rep2


title: VHIO179_284 rep1

tag: spike-in reference organsms


title: WT TEX rep3 stat

description: Terminator exonuclease (TEX) treated

tag: strain

value: wild-type

tag: phase

value: stationary


title: HCC1187_STAT3_ChIP-seq


title: WT TEX rep2 stat

description: Terminator exonuclease (TEX) treated


title: VHIO179_284 input

tag: spike-in cell line


title: DHT PDX HCI-009 3939

description: DHT 1


title: WT TEX rep1 stat

description: Terminator exonuclease (TEX) treated


title: Ctrl PDX HCI-009 3944

description: Control 2

value: Vehicle control:Cellulose pellet, 9wk


title: VHIO179_181 rep4


title: BT474_STAT3_ChIP-seq


title: VHIO179_181 rep3


title: Ctrl PDX HCI-009 3946

description: Control 3


title: MDA-MB-231_EtoH_4hr_REP3

data_processing:
TopHat v1.4.1 was used to align 50 million read pairs in the fastq files using with the options –r100 --mate-std-dev 75. GENCODE V9 was used as the transcriptome-index
Cufflinks v1.3.0 and BEDTools were used to calculate raw counts for each GENCODE transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table of reads counts per gene in each sample

growth_protocol: MDA-MB-231 cells were cultured in DMEM media, 10% FBS, 1 mM sodium pyruvate, non-essential amino acids. HCC70 cells were cultured in RPMI media, 10% FBS, 10 mM HEPES, 1 mM sodium pyruvate, 4.5 g/l glucose.

extract_protocol:
Cells were lysed with Buffer RL (Norgen Biotek) containing 10% beta-mercaptoethanol. Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek).
RNA-seq libraries for each sample were constructed from 250 ng total RNA using the polyA selection and transposase-based non-stranded library construction (Tn-RNA-seq) described previously (Gertz et al. Transposase mediated construction of RNA-seq libraries.2012. Genome Res 22 (1):134-141). Libraries were pooled and sequenced on an Illumina HiSeq 2000 sequencer using paired-end 50bp reads with a 6 bp index read.

treatment_protocol: Cells were treated with 100nM dexamethasone or an equal volume of 100% ethanol for four hours.

value: Ethanol

value: Basal-like breast cancer


title: WT TEX rep3 MLP

description: Terminator exonuclease (TEX) treated

value: mid-logarithmic


title: WT rep2

value: wild-type (tdk mutant background)


title: Ctrl PDX HCI-009 3943

description: Control 1


title: WT TEX rep2 MLP

description: Terminator exonuclease (TEX) treated


title: WT rep1


title: MDA-MB-231_EtoH_4hr_REP2


title: Choroid Plexus Org D53

first: Paula

last: Freire Pritchett

address: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus

institute: Medical Research Council

description:
SIGAE4
ChP sample 3
2 pooled choroid plexus organoids dissociated to single cells and run on one well of 10X chromium, then pooled for sequencing on two lanes S1 Illumina Novaseq

data_processing:
Raw sequencing output was converted to the standard fastq format by bcl2fastq, before running through CellRanger Count (version 3.1.0, 10X Genomics) which also performed read alignment using STAR with GRCh38 human reference genome.
Matrix files and metadata output from Cell Ranger 3.1.0 for each sample were fed into Seurat, and merged. Cells with %MT- genes greater than 30% were removed, as were cells with greater than 100000 nCount_RNA which were considered likely doublets. The data was then run through SCTransform for read normalization, data scaling, regression of mitochondrial genes and cell cycle genes, and variable feature finding.
Genome_build: GRCh38 human reference genome
Supplementary_files_format_and_content: SCTransformed merged matrix of all cells, .txt format

source_name: H1 human ES cell-derived organoids

growth_protocol: H9 or H1 cells were dissociated and used to generate either telencephalic organoids without the use of small molecules, or choroid plexus organoids by applying a pulse of Wnt agonist and Bmp after matrigel embedding and expansion.

extract_protocol:
Single cell dissociation was performed with Accumax _Dnase and Actinomycin D for 15-20 min at 37C with periodic flicking and then trituration every 5 min. Cells were filtered through a 50um filter and dead cells removed using Miltenyi Dead Cell Removal kit before running approximately 16,000 cells per sample lane through the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (10X Genomics, 120237) workflow. The reverse transcriptase reaction and subsequent amplification was carried out on a Thermal Cycler according to 10X Genomics manufacturer instructions. Libraries were quality tested before sequencing using a 2100 Bioanalyzer Instrument (Agilent).
Each sample was loaded onto separate wells of the 10X Chromium system and then pooled for subsequent sequencing on two lanes of an S1 flowcell on the Illumina Novaseq 6000.

treatment_protocol: Untreated (Telencephalon sample) or treated with CHIR99021 and BMP4 (ChP samples 1-3)

value: H1 human ES cell-derived organoids

tag: Stage

value: Day 53


title: VHIO179_181 rep1

value: Drosophila melanogaster

value: Drosophila S2 cells


title: MDA-MB-231_EtoH_4hr_REP1


title: Choroid Plexus Org D46

description:
SIGAG4
ChP sample 2
2 pooled choroid plexus organoids dissociated to single cells and run on one well of 10X chromium, then pooled for sequencing on two lanes S1 Illumina Novaseq

value: Day 46


title: WT TEX rep1 MLP

description: Terminator exonuclease (TEX) treated

tag: genotype


title: VHIO179_181 input

tag: cell type


title: Choroid Plexus Org D27

description:
SIGAF4
ChP sample 1
2 pooled choroid plexus organoids dissociated to single cells and run on one well of 10X chromium, then pooled for sequencing on two lanes S1 Illumina Novaseq

value: Day 27


title: MDA-MB-231_DEX_4hr_REP3

value: 100nM dexamethasone


title: WT TEX rep3 ELP

description: Terminator exonuclease (TEX) treated

value: early-logarithmic


title: MDA-MB-231_DEX_4hr_REP2


title: Telencephalon organoids

description:
SIGAC4
Telencephalon
2 pooled telencephalic organoids dissociated to single cells and run on one well of 10X chromium, then pooled for sequencing on two lanes S1 Illumina Novaseq

source_name: H9 human ES cell-derived organoids

value: H9 human ES cell-derived organoids

value: Day 55


title: AB577M rep4

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

value: BG4 single-chain antibody


title: AB577M input


title: WT TEX rep2 ELP

description: Terminator exonuclease (TEX) treated

value: wild-type


title: MDA-MB-231_DEX_4hr_REP1

value: Basal-like breast cancer


title: HIV-1 infected CEM NAT10 PAR-CLIP

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description:
Total RNA
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 0.12.7: bowtie -m 8 -a --best --strata --chunkmbs 10000
hg19 non-aligning reads aligned to the HIV-1 NL4-3 genome using Bowtie 0.12.7: bowtie -m 3 -v 1 -a --best --strata --chunkmbs 10000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Genome_build: NL4-3 genomes: 551-9626nt of GenBank AF324493.2
Supplementary_files_format_and_content: bed files, aligned to HIV-1 NL4-3 genome

source_name: HIV-1 infected CEM NAT10

extract_protocol:
PAR-CLIP (PA-ac4C-seq is PAR-CLIP done with the ac4C antibody directly UV crosslinked to it's target RNA)
All samples were processed with the NEB Next small RNA-seq kit

value: CEM

tag: virus

value: hIV-1 NL4-3

tag: genotype/variation

value: CEM clonally expressing FLAG-NAT10

tag: technique

value: PAR-CLIP

tag: pulldown antibody

value: anti-Flag, Sigma, Cat No F1804, Lot No SLBQ6349V


title: VHIO179_181 rep2

value: Drosophila melanogaster

value: Drosophila S2 cells


title: WT TEX rep1 ELP

description: Terminator exonuclease (TEX) treated


title: HIV-1 infected CEM GFP PAR-CLIP

source_name: HIV-1 infected CEM GFP

tag: cell line

value: CEM clonally expressing FLAG-GFP


title: WT rep3 stat

value: stationary


title: dNAT10 CEM virion RNA PA-ac4C-seq

description:
HIV-1 virion packaged RNA
Aligned to the HIV-1 NL4-3 genome, with one copy of LTR, U3 sequence on the 5' end, R-U5 on the 3' end

source_name: dNAT10 CEM virion RNA

value: NAT10 depleted CEM (clonaly expressing NAT10-targeting Cas9)

value: anti-ac4C, Abcam, ab252215, Lot No GR3269449-2


title: WT rep2 stat


title: HCC70_ETOH_4hr_REP2

source_name: HCC70 Cell line

value: Ethanol


title: STG316 rep3

value: breast cancer tissue


title: WT rep1 stat


title: HCC70_ETOH_4hr_REP1


title: AB577M rep2

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain


title: Control CEM virion RNA PA-ac4C-seq

source_name: Control CEM virion RNA

value: CEM clonally expressing non-targeting Cas9


title: AB577M rep1

source_name: fixed human breast cancer PDTX tissue

value: BG4 single-chain antibody


title: HCC70_DEX_4hr_REP3

value: 100nM dexamethasone

value: Basal-like breast cancer


title: WT rep3 MLP

value: wild-type

value: mid-logarithmic


title: AB636M input


title: AB577M rep3


title: WT rep2 MLP


title: STG143_317 rep3


title: HCC70_DEX_4hr_REP1


title: STG143_317 rep4


title: HCC70_ETOH_4hr_REP3


title: WT rep1 MLP


title: STG143_317 rep2


title: WT rep2 ELP

value: early-logarithmic


title: WT rep1 ELP


title: WT rep3 ELP


title: STG143_317 rep1


title: STG143_317 input


title: AB636M rep4


title: Replicate 3 Blood_Fed_day 3

city: Slingerlands

first: Dilip

middle: K

last: Nag

state: NY

address: 5668 State Farm Road

department: Division of Infectious Diseases

institute: Griffin Laboratory, Wadsworth Center, New York State Department of Health

description: RNA was isolated using mrVana miRNA kisolation kit

data_processing:
The raw sequences were subjected to quality check by FastQC
Bioinformatics analysis was carried out using CLC Genomics workbench v.20 software.
Gene expression tracks after mapping are shown
Genome_build: Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa.gz

organism: Aedes aegypti

source_name: Ovary

growth_protocol: 4-7 days old A. aegypti (from Poza Rica, Mexico) were fed with warmed sheep blood. No additional blood meals were given for the entire study period. Control mosquitoes were given sugar meal.

extract_protocol:
Total RNA was isolated using the mirVana miRNA isolation kit (Invitrogen) following the manufacturer’s suggestions.
RNA libraries were prepared following the Illumina Stranded total RNA library prep kit with Ribo-Zero Gold protocol.
Following library concentration and quality control, final libraries were pooled to 10 nM. After dilution and denaturing, the pooled library was loaded onto a NovaSeq6000 S1 flow cell (PE200) for sequencing.

treatment_protocol: All mosquitoes, both sugar fed and blood fed, were maintained with 10% sucrose and reared identically. Ovary samples were collected on day 3, 10, and 20 post blood meal (PBM) and stored immediately at -80oC.

tag: age

value: 4-7 day old mosquito

tag: diet

value: Fed with blood meal

tag: timepoint

value: Ovary collected on day 3 PBM


title: Replicate 4 Blood_Fed_day 20

value: Ovary collected on day 20 PBM


title: STG143_284 rep4

value: Drosophila melanogaster

value: Drosophila S2 cells


title: Replicate 4 Blood_Fed_day 10

value: Ovary collected on day 10 PBM


title: STG143_284 rep2


title: Replicate 4 Blood_Fed_day 3


title: HCC70_DEX_4hr_REP2

tag: treatment


title: Replicate 4 Sugar_Fed_day 20

value: Fed with sugar meal

value: Ovary collected on day 20 PSM


title: STG143_284 input

value: breast cancer tissue

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse strain

tag: chip antibody


title: AB636M rep3

value: BG4 single-chain antibody

tag: spike-in reference organsms


title: Replicate 4 Sugar_Fed_day 10

value: Ovary collected on day 10 PSM


title: Replicate 4 Sugar_Fed_day 3

value: Ovary collected on day 3 PSM


title: Replicate 2 Blood_Fed_day 10


title: AB636M rep2

tag: strain


title: Replicate 2 Blood_Fed_day 20


title: STG143_284 rep3


title: H4CAPE3 (mRNA-seq)

city: Chengdu

first: Ya

last: Luo

address: 17, 3rd Section, Renmin South Road

institute: Sichuan University

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software v2.20
miRNA sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using miRDeep2 v0.0.8 with parameters -e -j -h -l 18 -m
Processed data of miRNA was quantified using miRDeep2 v0.0.8 with parameters -t hsa
For mRNA data, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to GRCh38 and quantified using kallisto v0.46.1 with parameters -i transcripts.idx -b 100
Genome_build: GRCh38
Supplementary_files_format_and_content: CAPE_miRNA_raw_counts.csv:  Matrix table with raw miRNA counts for every miRNA and every sample
CAPE_mRNA_raw_gene_counts.csv:  Matrix table with raw gene counts for every gene and every sample
CAPE_mRNA_TPM.csv:  Comma-delimited text file includes TPM values for each Sample

source_name: small-cell lung cancer H446 cells

growth_protocol: H446 cells were cultured and maintained in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, USA) supplemented with 10% fetal bovine serum (FBS; Gibco), penicillin (100 U/ml; Beyotime, SH, China), and streptomycin (100 mg/ml; Beyotime). The cells were cultured in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols. Transcriptome sequencing was performed on an Illumina platform by Shanghai Personal Biotechnology Co. Ltd. Finally, 150-bp paired-end raw reads were obtained.

treatment_protocol: H446 cells were harvested for RNA extraction after 8 h of CAPE treatment at a concentration of 40 µM. The cells incubated with the same volume of DMSO as the CAPE (40 μM)-treated group were used as the control.

value: CAPE (40 μM in DMSO)


title: H4CAPE2 (mRNA-seq)


title: AB636M rep1


title: H4CAPE1 (mRNA-seq)


title: STG139M_284 rep4


title: Replicate 2 Blood_Fed_day 3


title: BMDC_UI_24hr_rep2

type: RNA

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

hyb_protocol: cRNA fragmentation and GeneChip hybridizations steps were carried out as described in Affymetrix procedure.

scan_protocol: GeneChipScanner (GSC) 3000 was used with GeneChip Operating Software (GCOS).

data_processing: The normalization of the data was performed with R and the RMA method of the affy Bioconductor package.

label: Biotin

source_name: Uninfected BMDCs sorted based on MHC class II expression.

label_protocol: Complementary RNA amplification and biotin labeling were performed according to Affymetrix protocols.

growth_protocol: Dendritic cells (BMDCs) were generated in vitro from bone marrow progenitors and Leishmania amazonensis amastigotes were purified from mouse cutaneous lesions. Amastigotes were left untreated or incubated with a mouse serum from L. amazonensis-infected mouse BALB/c.

extract_protocol: Total RNAs were extracted from biological triplicate BMDC cultures using the Rneasy Plus Mini kit (Qiagen) according to the manufacturer's instructions. Evaluation of RNA quality was performed by optical density measurement and by electrophoresis on a Lab-on-a-chip product using the Agilent 2100 Bioanalyzer (Agilent). RNA was quantified using Nanodrop (Kisker). Following quality controls (RIN > 7), RNAs were subjected to the Two-Cycle Target Labeling procedure according to the Manufacturer's recommendations.

treatment_protocol: BMDCs were left uninfected or infected with unopsonized or Ab-opsonized amastigotes. After 24h, and following a sorting procedure, only BMDCs housing living amastigotes were selected for total RNA extraction based on the expression of MHC class II (host cell) and DsRed2 (parasites) molecules.

value: BMDC

value: Balb/c

tag: agent

tag: time point

value: 24 hrs


title: H4Ctrl3 (mRNA-seq)

value: control (DMSO)


title: Replicate 2 Sugar_Fed_day 20

value: 4-7 day old mosquito


title: BMDC_aLV79-IS_24hr_rep3

source_name: BMDCs infected with L. amazonensis amastigotes opsonized with anti-Leishmania antibodies and sorted based on MHC class II and DsRed2 expression.

value: L. amazonensis


title: BMDC_aLV79-IS_24hr_rep2


title: BMDC_UI_24hr_rep3


title: H4Ctrl2 (mRNA-seq)


title: BMDC_aLV79-IS_24hr_rep1


title: BMDC_UI_24hr_rep1


title: STG143_284 rep1

data_processing:
Fastq files were trimmed from adapters using cutadapt (options: -q 20 -O 3 http://dx.doi.org/10.14806/ej.17.1.200, ver: 1.16) and aligned32 to a combined genome consisting of hg19 (H. Sapiens), dm6 (D. melanogaster) and mm10 (M.musculus) with bwa-mem (ver. 0.7.17-r1188). Bam files were generated from the alignment with samtools view (options: -Sb -F2308 -q 10, ver: 1.9) and subsequently split by organisms to obtain 3 bam files for each sample.
Duplicated reads were marked and removed using picard MarkDuplicates (ver: 2.20.3).
For all organisms, the total sequencing coverage (total recovery) was quantified as the total number of unique reads aligning to the respective genome
Standard peak calling was performed for each sample using MACS2 (ver. 2.1.2) with default options on hg19 and dm6 bam files respectively.
For each human PDTX model, peak regions were considered positive if confirmed in 2 out of 4 technical replicates (multi2) with bedtools v2.27.1 multiinter. All human confirmed G4-ChIP-seq peak files (multi2) of the 22 models were merged (bedtools merge) and regions more than 99 bp long retained to generate a single G4 DNA consensus of 26,103 G4 regions. Finally, the coverage of the samples was quantified over the consensus human set (bedtools coverage).
Reference normalization factor estimation and human ChIP signal normalization. For each PDTX biopsy, four technical qG4-ChIP experiments were performed and sequenced alongside one input chromatin (control). In each experiment, a similar amount of reference (D. melanogaster) chromatin from the same batch was added. To estimate PDTX normalization factors, reference coverage was determined at a pre-defined consensus consisting of 1,367 intervals (see Supplementary Data 2). The reference consensus set was defined from, and covers, G4-enriched regions observed in more than 110 pull-down experiments. The normalization factor of each ChIP sample has been defined as the ratio between the maximum observed coverage (across all ChIP samples) and the individual sample coverage. Note that only ChIP experiments were used for this step (i.e. inputs are excluded and forced to 1). . The normalization factors were then exported and used as input for a customized R script performing the normalization of the human signal. For each G4-ChIP-seq experiment, human signal (i.e. read coverage within human G4 consensus) was quantified by performing input subtraction and normalization with their respective reference reads and human library sizes. To assess if the normalization step has globally improved the experimental reproducibility, a quantitative parameter, the Improvement Factor IF, was devised that measures both the increase (i.e. improvement) in data similarity  between experiments corresponding to the same technical and biological samples and the increase dissimilarity between different samples. Specifically, the improvement factor of each biological sample has been estimated as: IF = sum_N(D_ratio_inter) - sum_N(D_ratio_intra).  Where: o  D_ratio: euclidean_distance_after_normalization/euclidean_distance_before_normalization;  o  N: total N. ChIP samples  o  euclidean_distance_after_normalization: Euclidean similarity matrix computed on input  subtracted, library size adjusted, drosophila normalized data and rescaled to its  maximum value;  o  euclidean_distance_before_normalization: Euclidean similarity matrix computed on input  subtracted, library size adjusted data and rescaled to its maximum value;   o  D_ratio_inter: similarity values among samples belonging to the same technical or  biological group;   o  D_ratio_intra: similarity values among samples not belonging to the same  technical or biological group;   135 individual samples (ChIP + Input) were processed from 22 different PDTX models. Some   PDTX models have more than one biological sample.
Genome_build: hg19, dm6, mm10
Supplementary_files_format_and_content: bigwig files  *nodup.w10.rpm.bw were generated from the duplicates removed bam files binning the regions in 10bp windows and normalizing the coverage in those regions by the total number of unique reads. The bigwig files *nodup.dm6.sorted.bw were generated starting from **nodup.w10.rpm.bw and following those steps: 1. bw converted to begraph; 2.using bedtools unionbedg  perform input subtraction (pull-down minus input RPM) and multiply by drosophila normlization factors.

extract_protocol:
PDTX chromatin prep and G4-ChIP-seq: Briefly, D. melanogaster S2 cells were cultured in Schneider's Drosophila Medium (Thermo Fisher Scientific, cat no. R69007) containing 10% fetal bovine serum (FBS) Medium (Thermo Fisher Scientific, cat no. 10500064). To prepare spike-in Drosophila chromatin, 100 million cells were i) harvested by centrifugation, ii) fixed for 10 min in a solution of media containing 10 % FBS, 1% Formaldehyde (Thermo Fisher Scientific, cat no. 28908) and iii) quenched for 5 min by addition of 125 mM glycine (Fisher Scientific, cat no. 11545005). The cell pellet was washed with 10 mL PBS, pelleted by centrifugation and subsequently stored on ice for the lysis procedure. The 2-step chromatin lysis procedure was performed according to the Chromatrap procedure ("Spin column ChIP kit for qPCR v6.4"). 500 µL intact chromatin was sonicated into 100-500 bp fragments using a Bioruptor Plus (Diagenode cat. no. B02010003 with cooling) at 4C. Sonicated chromatin was diluted with 1.5 mL lysis buffer (Chromatrap cat no. 100005) before snap-freezing as 25 µL aliquots. PDTX chromatin was prepared essentially as described in Schmidt et al. (Methods 2009)30. Briefly, a snap-frozen PDTX biopsy, ~1 cm3, was transferred into a 50 mL falcon tube, on dry-ice, and crushed into smaller chunks on dry-ice using a scalpel followed by fixation for 20 min in 30 ml solution A, containing 1% formaldehyde, and then quenched for 5 min by adding 125 mM glycine. The supernatant of the pelleted tissue was discarded, and the pellet washed twice with 10 mL ice-cold PBS before resuspending in 1 mL PBS and transferred to a 1 mL glass Douncer (Fisher scientific, cat no. 11591295). 10 strokes were employed for each douncing step with a loose and then tight pestle, and the remaining tissue slurry was transferred to a 15 mL tube, centrifuged for 5 min at 2500xg and subjected to lysis according to Schmidt et al30. Briefly, after the 10 mL LB2 treatment and nuclei pelleting step, the pellet was resuspended in 500 µL LB3 and LB3-chromatin solution split into two Bioruptor TBX (Diagenode, cat no. C30010010-300) sonication tubes. The samples were sonicated until the desired fragment length (100-500 bp) was achieved. Finally, 50 µL of a 10% Triton X-100 LB3 solution was mixed with the sonicated solution and aliquoted into 50 µL aliquots before snap-freezing in liquid nitrogen. 5 μL of PDTX chromatin was quantified by Qubit using the "broad range kit" (Thermo Fisher Scientific, cat. no. Q32853). In each qG4-ChIP-seq reaction, 225ng of PDTX chromatin, 102ng of spike-in drosophila chromatin and 2% RNaseA (Invitrogen, cat. no. AM2271) in blocking buffer (25mM HEPES, pH 7.5, 10.5mM NaCl, 110mM KCl, 1mM MgCl2 and 1% BSA (Merck, cat. no. A7030) in Milli-Q water were mixed and incubated at 37C for 30min at 800rpm. All PDTX chromatin batches containing a different concentration than 30 ng/μL were balanced to the same level, either by dilution with LB3 containing 1% Triton X-100 or by up-scaling the ChIP reaction. For PDTX chromatin with a concentration of 30 ng/μL, 7.5 μL of the PDTX chromatin was added to a solution containing 270 μL blocking buffer including 2% RNase A and 7.5 μL spike-in drosophila chromatin. After RNaseA treatment, 15 μL of 2M BG4, prepared as described previously31, was added to each qG4-ChIP-seq reaction and the reaction mixture shaken at 1,400 rpm at 16C for 1 hour. Meanwhile, 65 μL of anti-FLAG magnetic beads (Sigma-Aldrich, cat. no. M8823) were washed three times with 650 μL of blocking buffer and resuspended in 1,300 μL blocking buffer. The pre-washed beads were incubated at 16C at 1,400rpm and 300 μL of pre-washed beads added to the reaction mixture after BG4 incubation. The reaction mixture with beads was incubated at 16C for 1 hour at 1,400rpm. Then, the beads were washed four times in 400 μL cold wash buffer (100mM KCl, 0.1% Tween 20 and 10mM Tris, pH 7.4 in Milli-Q water) in the cold room and twice at 37C for 15min at 1,400rpm, followed by one cold wash on magnetic stand. The enriched chromatin on beads was resuspended in 75 μL TE buffer and 1 μL Proteinase K (Invitrogen, cat. no. AM2546) added. 6 μL Proteinase K was added to input sample which refers to a qG4-ChIP-seq reaction mixture without BG4 and beads. The reaction mixture was incubated at 65C for 3 hours at 1,400 rpm and purified using QIAGEN MinElute Kit (QIAGEN, cat. no. 28206).
Purified DNAs were subjected to Nextera DNA library preparation.For 40 μL library preparation reaction, 3-5ng of the ChIP or input DNA (Qubit high sensitivity kit, Thermo Fisher Scientific, cat. no. Q32854), 20 μL 2X tagmentation buffer (Illumina, cat. no. 15027866), 1.25 μL Tn5 enzyme (Illumina, cat no. 18027865) and nuclease-free water was incubated at 37°C for 20min at 800rpm. The reaction mixture was purified using QIAGEN MinElute Kit (QIAGEN, cat. no. 28206) according to the manufacturer’s instruction and eluted in 20 μL EB buffer. To amplify the library, 20 μL of the DNA was then mixed with 25 μL NEB Next High Fidelity 2X PCR Master Mix (New England Biolabs, cat. no. N0541S), 2.5 μL Nextera index kit i5 primer (Illumina, cat. no. 15055290) and 2.5 μL Nextera index kit i7 primer (Illumina, cat. no. 15055290). The PCR program was as follows: 72°C for 5 minutes, 98°C for 30 seconds, followed by 8 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Libraries were quantified using a Bioanalyzer (Agilent) to estimate the average library size and concentration determined via Qubit HS. The library concentration was corrected for the library size using the following relationship:1 ng/µL = 3nM = 500 bp. Samples were subjected to single-end sequencing with a read length of 75bp on an Illumina NextSeq instrument.”

value: Drosophila melanogaster

tag: spike-in cell line


title: BMDC_aLV79_24hr_rep1

source_name: BMDCs infected with L. amazonensis unopsonized amastigotes and sorted based on MHC class II and DsRed2 expression.


title: BMDC_aLV79_24hr_rep2


title: BMDC_aLV79_24hr_rep3


title: Replicate 2 Sugar_Fed_day 10


title: STG139M_284 rep2

value: Drosophila S2 cells


title: H4Ctrl1 (mRNA-seq)


title: Replicate 2 Sugar_Fed_day 3


title: H4CAPE2 (miRNA-seq)


title: mC_Ephydatia_muellerii_WGBS

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

data_processing:
CASAVA v1.8.2
For Bisulfite-seq, adapters were trimmed using fastp as default, then aligned to the reference genome using Bowtie2 and BSseeker2 with the option --bt2--end-to-end. PCR duplicates were removed using Sambamba v.0.6.6 before methylation quantification with BSseeker2.
Genome_build: Ephydatia muelleri genome assembly was obtained from https://www.ncbi.nlm.nih.gov/bioproject/PRJNA579531
Supplementary_files_format_and_content: Bisulfite-seq files (CGmap files) are the direct output from BSseeker2 (https://github.com/BSSeeker/BSseeker2), they contain chromosome position, (1) chromosome  (2) nucleotide on Watson (+) strand  (3) position  (4) context (CG/CHG/CHH)  (5) dinucleotide-context (CA/CC/CG/CT)  (6) methylation-level = #_of_C / (#_of_C + #_of_T). (7) #_of_C (methylated C, the count of reads showing C here) (8) = #_of_C + #_of_T (all Cytosines, the sum of reads showing C or T in that position).

organism: Ephydatia muelleri

extract_protocol:
Phenol-chloroform extraction
Genomic DNA was fragmented with a Covaris S2 sonicator to a mean length of 200 bp, then end-repaired, A-tailed, ligated to methylated Illumina TruSeq adapters, bisulfite converted and subjected to 7 cycles of PCR amplification with KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).

value: collected from Sooke Reservoir, City of Victoria, Canada