title: LeLab_B1H_seq_preselection_replicate2

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

description: plasmid DNA

data_processing:
Library strategy: B1H-Seq
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Escherichia coli MG1655 reference genome using Bowtie 113 and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 MG1655-bowtie --sam *.fastq > output.sam  Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools14 using the following command: bedtools genomecov -d -ibam output.sorted.bam -g Ecoli_MG1655.fna > coverage_output.txt  ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts. To calculate the enrichment of reads at the parS or NBS site, we summed the RPBPM values for a 100bp window surrounding the parS or NBS site.
We used fastx_trimmer script from the FASTX-Toolkit16 to remove nucleotides 0 to 20 and 114 to 150 from our reads using the following command: fastx_trimmer -f 20 -l 114 -Q33 -i TLE4_S4_R1_001.fastq -o TLE4_trimmed.fastq. Subsequently, we discarded sequence reads with an average Phred score <28, using the fastq_quality_filter script in the FASTX-Toolkit: fastq_quality_filter -v -Q33 -q 28 -p 100 -i TLE4_trimmed -o TLE4_trimmed_filtered.fastq. Reads were further filtered for the exact match to the following sequence:[ATGC][ATGC][GC]tctcacgtagcgaat[ATGC][ATGC][GC]atgcgtcttctt[ATGC][ATGC][GC]ttgccggacgaggtacagtcctatcttgtgagtggagagctgacagcg[ATGC][ATGC][GC]. Corresponding codons (bases 1-3, 19-21, 34-36, 85-87) for the four specificity residues were extracted from the above 87-bp nucleotide sequence, and subsequently translated to amino acid sequence, following the standard genetic code. Variants with stop codon (TAG) were removed and were not considered in subsequent steps. Because of a high reproducibility among replicates, we pooled reads from three replicates together. We counted the number of occurrences (counts) for each unique variant, and removed variants with less than 10 reads (Fig. S7B). Greater than 94% of the predicted variants were represented by at least 10 reads. The variant counts for pre-selection and post-selection (for parS- or NBS-binding) libraries were used in the following steps to estimate the fitness score of each variant.
We calculated the fitness of each variant (ƒparS and ƒNBS), in comparison to WT variants (RTAG or QKKR), as described previously17,18.   ƒparS, raw = log10(N variant, parS post-selection library / N wt, parS post-selection library) -  log10(N variant, pre-selection library / N wt, pre-selection library)  N variant, parS post-selection library = counts of each variant in the post-selection library for binding to parS.   N wt, parS post-selection library = counts of the WT (RTAG) in the post selection library for binding to parS.  N variant, pre-selection library = counts of each variant in the pre-selection (starting) library.   N wt, pre-selection library = counts of the WT (RTAG) in the pre-selection (starting) library.    ƒNBS, raw = log10(N variant, NBS post-selection library / N wt, NBS post-selection library) -  log10(N variant, pre-selection library / N wt, pre-selection library)  N variant, NBS post-selection library = counts of each variant in the post-selection library for binding to NBS.   N wt, NBS post-selection library = counts of the WT (QKKR) in the post selection library for binding to NBS.  N variant, pre-selection library = counts of each variant in the pre-selection (starting) library.   N wt, pre-selection library = counts of the WT (QKKR) in the pre-selection (starting) library.  These raw fitness scores were further transformed so that ƒparS of the RTAG variant was 1 and that of QKKR variant was 0, and ƒNBS of the RTAG variant was 0 and that of QKKR variant was 1. The fitness scores for every variant were presented in the fitness scatterplot. Dark green:  strong parS binding, no NBS binding (fitness score: ƒparS≥0.65, ƒNBS≤0.2); light green: strong parS binding, weak to medium NBS binding (ƒparS≥0.65, 0.2≤ƒNBS≤0.65); magenta: strong NBS binding, no parS binding (ƒNBS≥0.65, ƒparS≤0.2); pink: strong NBS binding, weak to medium parS binding (ƒNBS≥0.65, 0.2≤ƒparS≤0.65); black: promiscuous (ƒNBS≥0.65, ƒparS≥0.65). Frequency logos of each class of variants were constructed using WebLogo v3.03
Genome_build: NC_000913.3
Supplementary_files_format_and_content: The processed data files for ChIP-seq are tab-delimited files containing three fields, the genome build, the nuclotide position, and the coverage at that position. The processed data files for B1H-seq are tab-delimited files containing three fields, the coutn of the ParB variants, and the identity that variant.

organism: Escherichia coli

source_name: Escherichia coli USO rpoZ- hisB- pyrF-

growth_protocol: For E. coli ChIP-seq, cells harboring pUT18C-1xFLAG-ParB/Noc were grown in LB (25 mL) at 28oC to mid exponential phase (OD600 ~0.4) before 1 mM IPTG was added for 1-3 hours. The induction time (either 1, 2 or 3 hours) was chosen so that all ParB/Noc variants were produced to same protein level as judged by an α-FLAG Western blot. Subsequently, formaldehyde is added to a final concentration of 1% to fix the cells. For B1H-seq (deep mutational scanning experiments), The selection strain TLE3001 (USO rpoZ- hisB- pyrF-) harboring either pU3H3::19bp-NBS or pU3H3::19bp-parS plasmid was made electrocompetent. Next, approximately 2 µg of the combinatorial plasmid library were electroporated into 100 µL of the selection strain. The procedure was repeated for four more times, and electroporated cells were recovered in 10 mL of LB for an hour at 37oC. Subsequently, cells were washed off rich LB medium and resuspended in 5ml of 1x M9 liquid. Cells were then plated out on ten 150 mm Petri plates containing M9 -histidine medium supplemented with 0.1 mM IPTG, 5 mM 3-AT (a competitive inhibitor of HIS3 protein, used to increase the stringency of the selection), and appropriate antibiotics. Plates were incubated at 37oC for 48 hours before cells were scrapped off the agar surface and pooled together.

extract_protocol:
For ChIP-seq, DNA was isolated using Qiagen PCR purification columns. For B1H-seq, plasmid DNA was isolated using Qiagen MiniPrep columns. Detailed protocols are listed in the Supplementary Materials
For ChIP-seq libraries, a standard library construction procedure (using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina sequencing) was employed. For B1H-seq, a similar strategy to amplicon-seq was used to construct libraries for Illumina sequencing. Briefly,Illumina Truseq-compatible libraries were constructed from pre- and post-selection plasmid libraries via two rounds of PCR.  PCR round 1:  Primer 4nns_R (10 µM): 2.5 µL  Mixture in equimolar amount of primers 4nns_offset_0_F; 4nns_offset_1_F; 4nns_offset_2_F; 4nns_offset_3_F; 4nns_offset_4_F (10 µM): 2.5 µL. A mixture of forward primers were used to stagger reads across the amplicon to improve the distribution of base calls at each position during the initial rounds of Illumina sequencing.  dNTP (10mM): 1 µL  DMSO: 1.5 µL  Plasmid template (pre- or post-selection): 1 µL of 500 ng/µL  Phusion polymerase: 0.5 µL  5x HF buffer: 10 µL  Water: 31 µL  PCR program: 98oC for 30s, (98oC for 10s, 56oC for 20s, 72oC for 10s) x 20 cycles, 72oC for 5min.  PCR products were gel-purified, quantified by Qubit hsDNA quantification kit (ThermoFisher), and used as template in the second PCR.  PCR round 2:  NEBNext Index primer (NEB): 2.5 µL  NEBNext universal primer (NEB): 2.5 µL  dNTP (10mM): 1 µL  DMSO: 1.5 µL  Template: 5 µL of gel-purified DNA from PCR round 1  5x HF buffer: 10 µL  Phusion polymerase: 0.5 µL  Water: 27 µL  PCR program: 98oC for 30s, (98oC for 10s, 54oC for 20s, 72oC for 10s) x 12 cycles, 72oC for 5min.  PCR products were gel-purified, quantified by Qubit hsDNA quantification kit (ThermoFisher), and were sequenced on the Illumina HiSeq 2500 (single-end, 150 bp read length, 15% spike-in phiX DNA) at the Tufts University Genomics facility.

treatment_protocol: colonies were selected on M9 minimal medium lacking histidine (but supplemented with 5mM 3-AT)

tag: growth phase

value: mixed population, colonies pooled together

value: Escherichia coli USO rpoZ- hisB- pyrF- + pB1H2-w2::Caulobacter ParB variants + pU3H3::19bp-parS


title: WB_exp2_Treated_Patient1

status: Public on Aug 05 2019

type: RNA

city: Milan

first: Michaela

last: Fakiola

address: Via Francesco Sforza 35

country: Italy

institute: INGM

description:
Experiment 2
SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data were analyzed using lumi, beadarray and limma R packages. Raw data underwent background correction using negative ccontrol probes followed by quantile normalization and log2 transformation. Non-expressed (detection P-value > 0.05 in all arrays) and poor quality probes previously shown to have unreliable annotation were removed. Active Case versus i) Treated or ii) Healthy Controls contrasts were analyzed for differential expression against the fitted linear model using eBayesfunctions in limma.
Matrix non-normalised: software computed raw signal intensity

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: Biotinylated cRNA was generated following manufacturer protocols.

extract_protocol: RNA from whole blood samples was extracted using PAXgene Blood RNA kits (QIAGEN GmbH, Germany) according to manufacturer’s instructions. Globin mRNA was depleted using GLOBINclear™-Human kits (ThermoFischer Scientific, USA). RNA integrity and purity were checked using Tape Station 4200 (Agilent Technologies, USA).

tag: disease state

value: Active Visceral Leishmaniasis Case, treated with a single dose of liposome-encapsulated Amphotericin B

tag: gender

value: Male

tag: age


title: Donor_A_day_18 [A11.D18]

city: Paris

first: Aonghus

last: Lavelle

address: Faculte de medecine, 27 Rue de Chaligny

country: France

institute: Centre de Recherche Saint-Antoine/Sorbonne Universite

description: Humanized donor A, day 18 post 7 days of antibiotics

hyb_protocol: 600ng of Cy3-labeled cRNA per sample (specific activity > 11.0 pmol Cy3/µg of cRNA) was fragmented for 30minutes at 60 degrees Celsius, followed by hyrbridization at 65 degrees celsius for 17 hours in a rotating hybridization oven (Agilent technologies). This was followed by washing and drying.

scan_protocol: Slides were scanned with a G2565CA Scanner System (Agilent Technologies). This had a resolution of 3 micrometers and a dynamic range of 20 bit.

data_processing: Tiff image files were analyzed with the Feature Extraction Software .7.3.1 (Agilent technologies) using the GE1_107_Sep09 protocol, log2-transformed and quantile-normalized for the data in the matrix table.

organism: Mus musculus

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared with 100ng of total RNA with the One-Color Low Input Quick Amp Labeling Kit (Agilent technologies) according to the recommended protocol. Yields of cRNA and specific activities were assessed with the NanoDrop ND-1000 (Thermo Fisher Scientific). The array used was the SurePrint G3 Mouse GE 8 x 60K Microarray (Design ID: 028005, Agilent Technologies).

growth_protocol: Germ-free mice, humanized with fecal samples from one of two healthy human donors were maintained in isolators.

extract_protocol: Total RNA was extracted from mouse colon samples using the Rneasy® Mini Kit (Qiagen, Courtaboeuf, France) according to manufacturer’s instructions. RNA integrity was assessed using a Bioanalyzer 2100 with RNA 6000 Nano chips (Agilent technologies).

treatment_protocol: 56 days post humanization, 3 mice per donor group were euthanized and were sampled at baseline (day 0), followed by administration of amoxicillin/clavulanic acid (80mg/10mg) once per day for 7 days. This was followed by euthanasia and sampling of 4 mice per donor group at days 8, 11 and 18.

tag: tissue

value: Colon

tag: colonisation

value: Humanized germ free

value: 16 weeks

tag: day

tag: donor

value: A


title: SUPT1-KPT-1

type: SRA

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

description: SUPT-1 cell line - KPT treatment

library_source: transcriptomic

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with HiSat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Homo Sapiens (GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

source_name: T-ALL cell line

extract_protocol:
processed with QuantSeq Kit according to manufacturers instructions
all libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: protocol

value: RNA sequencing

tag: agent

value: KPT


title: MD-3-Lin-KO-1

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

data_processing:
The reads were trimmed using trim galore (v 0.4.1) to remove adapters.
The trimmed data were mapped to mouse genome (mm10) by tophat software (v 2.0.13) with default parameters
The read pair numbers mapped to each gene in the Refseq gene annotation (downloaded from UCSC genome browser in 03/2017) were calculated with HTseq (v 0.6.1)
The Fragments Per Kilobase of transcript per Million (FPKMs) for each gene were calculated using cufflinks package
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include raw counts for each gene in each sample

source_name: bone marrow cells

extract_protocol:
LSK and MPP cells were sorted from pooled bone marrow of two 10-week-old Tet2 Mut, Tet2 KO and wild-type mice by FACS. RNA was extracted using QIAGEN RNAeasy Kit.
RNA was amplified and barcoded and used to prepare libraries of two technical replicates, with ERCC spike in controls.

tag: strain

tag: developmental stage

value: bone marrow


title: WB_exp1_ActiveCase_Patient11

description:
Experiment 1
SAMPLE 34

data_processing:
Data were analyzed using lumi, beadarray and limma R packages. Raw data underwent background correction using negative ccontrol probes followed by quantile normalization and log2 transformation. Non-expressed (detection P-value > 0.05 in all arrays) and poor quality probes previously shown to have unreliable annotation were removed. Active Case versus i) Treated or ii) Healthy Controls contrasts were analyzed for differential expression against the fitted linear model using eBayes functions in limma.
Matrix non-normalised: software computed raw signal intensity

value: Active Visceral Leishmaniasis Case

value: Female


title: WB_exp1_EHC_Rep6

description:
Experiment 1
SAMPLE 36

value: Endemic Healthy Control (serology and quantiferon negative)


title: WB_exp2_ActiveCase_Patient1

description:
Experiment 2
SAMPLE 1


title: Donor_B_day_18 [B11.D18]

description: Humanized donor B, day 18 post 7 days of antibiotics

value: B


title: WB_exp2_ActiveCase_Patient2

description:
Experiment 2
SAMPLE 5


title: SUPT1-KPT-3

description: SUPT-1 cell line - KPT treatment


title: Donor_A_day_18 [A21.D18]


title: WB_exp1_Quantiferon_Rep8

description:
Experiment 1
SAMPLE 33

value: Quantiferon positive asymptomatic


title: Donor_A_day_18 [A22.D18]


title: LeLab_B1H_seq_preselection_replicate1

country: United Kingdom

description: plasmid DNA

library_source: genomic

molecule: genomic DNA

tag: genotype


title: WB_exp1_Treated_Patient10

description:
Experiment 1
SAMPLE 32

value: Active Visceral Leishmaniasis Case, treated with 15 doses of non-liposomal Amphotericin B on alternate days


title: WB_exp1_Treated_Patient11

description:
Experiment 1
SAMPLE 35


title: H3K27ac_ChIPseq_Ctrl_2

city: Copenhagen

first: Nils

middle: Billestrup

last: Billestrup

address: Bledamsvej

country: Denmark

institute: University of Copenhagen

description: mouse islets H3K27ac ctrl rep2

data_processing:
The single-end 50 base pair reads were mapped to the UCSC mouse transcriptome (mm9) by bowtie, allowing for up to 2 mismatches.
Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
in homer, function "makeUCSCfile" was used to generate bigWig file
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: pancreatic islets

growth_protocol: Isolated pancreatic islets were cultured in RPMI 1640 medium with 11mmol/l D-glucose supplemented with 2% human serum and 1 % penicillin/steptomycin. Medium and IL1B were changed every 5th day

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using KAPA DNA Library Preparation Kits for Illumina.

treatment_protocol: Islets were cultured in the absence or presence of 50pg/ml IL1B

tag: treatment

value: Ctrl 10d

value: male

value: 12 weeks

value: pancreatic islets

tag: chip antibody

value: H3K27ac (Cat#39133 Active Motif)


title: LeLab_B1H_seq_preselection_replicate3

description: plasmid DNA

value: mixed population, colonies pooled together

value: Escherichia coli USO rpoZ- hisB- pyrF- + pB1H2-w2::Caulobacter ParB variants + pU3H3::19bp-parS


title: Donor_B_day_18 [B21.D18]

value: Colon

value: Male

value: Humanized germ free

value: 16 weeks


title: WB_exp1_ActiveCase_Patient9

description:
Experiment 1
SAMPLE 31

value: Active Visceral Leishmaniasis Case


title: SUPT1-DEX-3

description: SUPT-1 cell line - DEXA treatment

value: RNA sequencing

value: DEXA


title: SUPT1-DEX-2

description: SUPT-1 cell line - DEXA treatment


title: Donor_B_day_18 [B22.D18]

value: B


title: LeLab_B1H_seq_postselection_parS_replicate1

description: plasmid DNA

value: Escherichia coli USO rpoZ- hisB- pyrF- + pB1H2-w2::Caulobacter ParB variants + pU3H3::19bp-NBS


title: LeLab_B1H_seq_postselection_parS_replicate2

description: plasmid DNA


title: Donor_B_day_18 [B12.D18]


title: SUPT1-DEX-1

description: SUPT-1 cell line - DEXA treatment


title: SUPT1-DMSO-3

description: SUPT-1 cell line - DMSO treatment

value: DMSO


title: RNA-seq MD2-RW2 ESC (Rinf Wild type Replicate #2)

data_processing:
ChIP-seq analysis: Raw data files are untrimmed fastq files generated using picard-tools (files ending in fastq.gz files), trimmed fastq files generated using trim-galore (v 0.4.1, https://github.com/FelixKrueger/TrimGalore). Reads were mapped to the mouse genome (mm10) using the software Bowtie2 (VN: 2.2.3) with default parameters (Langmead and Salzberg, 2012). The Rinf binding peaks were called by the software MACS2 using the input as controls (Zhang et al., 2008), with the final peaks from the merged reads of the two biological replicates.
RNA-seq analysis: The reads were trimmed using trim-galore to remove adapters and then mapped to mouse genome (mm10) by tophat software (v 2.0.13) with default parameters (the same to the ChIP-seq data mapping). The reads  mapped to each gene in the Refseq gene annotation (downloaded from UCSC genome browser in 03/2017) were calculated with HTseq (v 0.6.1, (Anders et al., 2015)) using “–s reverse” parameter to obtain read counts for each gene. The Fragments Per Kilobase of transcript per Million (FPKMs) for each gene were calculated using cufflinks package (v 2.2.1, (Trapnell et al., 2010)).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage (deeptools 3.1.0), gene expression FPKM were generated from cuffdiff (cufflinks v2.2.1).

source_name: RNA-seq Rinf Wild type mESC (Rinf Wild type Replicate #2)

growth_protocol: ESCs were cultured on gelatin in Serum/LIF and then harvested for ChIP-seq or RNA-seq

extract_protocol:
For RNA-seq, RNA extraction was performed using Omega E.Z.N.A Total RNA kit
ChIP-seq libraries were prepared using NEB library kit. RNA-seq libraries were prepared using illumina library prep kit following manufacterer's protocols at Einstein Epigenomcis core.

treatment_protocol: For ChIP-seq, ESCs were crosslinked, lysed, sonicated and subjected to ChIP using an anti-Rinf antibody (84546S, CST).

tag: Stage

value: mESC

tag: cell type

value: Embryonic stem cells

tag: passages

value: mixed 129/C57BL/6

value: Rinf Wild type


title: SUPT1-DMSO-2

description: SUPT-1 cell line - DMSO treatment


title: LeLab_B1H_seq_postselection_NBS_replicate3

description: plasmid DNA

treatment_protocol: colonies were selected on M9 minimal medium supplemented with histidine

tag: growth phase

value: Escherichia coli USO rpoZ- hisB- pyrF- + pB1H2-w2::Caulobacter ParB variants (starting library)


title: LeLab_B1H_seq_postselection_parS_replicate3

description: plasmid DNA

value: mixed population, colonies pooled together


title: LeLab_B1H_seq_postselection_NBS_replicate2

description: plasmid DNA


title: Donor_A_day_18 [A12.D18]

tag: gender

tag: age

value: A


title: 697-Combi-3

description: 697 cell line - DEXA+KPT treatment

source_name: B-ALL cell line

value: DEXA+KPT


title: LeLab_B1H_seq_postselection_NBS_replicate1

description: plasmid DNA


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Xanthomonas_campestris_ParB

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Escherichia coli MG1655 reference genome using Bowtie 113 and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 MG1655-bowtie --sam *.fastq > output.sam  Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools14 using the following command: bedtools genomecov -d -ibam output.sorted.bam -g Ecoli_MG1655.fna > coverage_output.txt  ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts. To calculate the enrichment of reads at the parS or NBS site, we summed the RPBPM values for a 100bp window surrounding the parS or NBS site.
We used fastx_trimmer script from the FASTX-Toolkit16 to remove nucleotides 0 to 20 and 114 to 150 from our reads using the following command: fastx_trimmer -f 20 -l 114 -Q33 -i TLE4_S4_R1_001.fastq -o TLE4_trimmed.fastq. Subsequently, we discarded sequence reads with an average Phred score <28, using the fastq_quality_filter script in the FASTX-Toolkit: fastq_quality_filter -v -Q33 -q 28 -p 100 -i TLE4_trimmed -o TLE4_trimmed_filtered.fastq. Reads were further filtered for the exact match to the following sequence:[ATGC][ATGC][GC]tctcacgtagcgaat[ATGC][ATGC][GC]atgcgtcttctt[ATGC][ATGC][GC]ttgccggacgaggtacagtcctatcttgtgagtggagagctgacagcg[ATGC][ATGC][GC]. Corresponding codons (bases 1-3, 19-21, 34-36, 85-87) for the four specificity residues were extracted from the above 87-bp nucleotide sequence, and subsequently translated to amino acid sequence, following the standard genetic code. Variants with stop codon (TAG) were removed and were not considered in subsequent steps. Because of a high reproducibility among replicates, we pooled reads from three replicates together. We counted the number of occurrences (counts) for each unique variant, and removed variants with less than 10 reads (Fig. S7B). Greater than 94% of the predicted variants were represented by at least 10 reads. The variant counts for pre-selection and post-selection (for parS- or NBS-binding) libraries were used in the following steps to estimate the fitness score of each variant.
We calculated the fitness of each variant (ƒparS and ƒNBS), in comparison to WT variants (RTAG or QKKR), as described previously17,18.   ƒparS, raw = log10(N variant, parS post-selection library / N wt, parS post-selection library) -  log10(N variant, pre-selection library / N wt, pre-selection library)  N variant, parS post-selection library = counts of each variant in the post-selection library for binding to parS.   N wt, parS post-selection library = counts of the WT (RTAG) in the post selection library for binding to parS.  N variant, pre-selection library = counts of each variant in the pre-selection (starting) library.   N wt, pre-selection library = counts of the WT (RTAG) in the pre-selection (starting) library.    ƒNBS, raw = log10(N variant, NBS post-selection library / N wt, NBS post-selection library) -  log10(N variant, pre-selection library / N wt, pre-selection library)  N variant, NBS post-selection library = counts of each variant in the post-selection library for binding to NBS.   N wt, NBS post-selection library = counts of the WT (QKKR) in the post selection library for binding to NBS.  N variant, pre-selection library = counts of each variant in the pre-selection (starting) library.   N wt, pre-selection library = counts of the WT (QKKR) in the pre-selection (starting) library.  These raw fitness scores were further transformed so that ƒparS of the RTAG variant was 1 and that of QKKR variant was 0, and ƒNBS of the RTAG variant was 0 and that of QKKR variant was 1. The fitness scores for every variant were presented in the fitness scatterplot. Dark green:  strong parS binding, no NBS binding (fitness score: ƒparS≥0.65, ƒNBS≤0.2); light green: strong parS binding, weak to medium NBS binding (ƒparS≥0.65, 0.2≤ƒNBS≤0.65); magenta: strong NBS binding, no parS binding (ƒNBS≥0.65, ƒparS≤0.2); pink: strong NBS binding, weak to medium parS binding (ƒNBS≥0.65, 0.2≤ƒparS≤0.65); black: promiscuous (ƒNBS≥0.65, ƒparS≥0.65). Frequency logos of each class of variants were constructed using WebLogo v3.03
Genome_build: NC_000913.3
Supplementary_files_format_and_content: The processed data files for ChIP-seq are tab-delimited files containing three fields, the genome build, the nuclotide position, and the coverage at that position. The processed data files for B1H-seq are tab-delimited files containing three fields, the coutn of the ParB variants, and the identity that variant.

source_name: Escherichia coli AB1157

treatment_protocol: FLAG-ParB were produced by addition of 1mM IPTG before formadehyde to 1% (final concentration ) was added to fix cells for ChIP-seq

value: mixed population, exponential phase


title: WB_exp1_Treated_Patient8

description:
Experiment 1
SAMPLE 29

tag: disease state

value: Active Visceral Leishmaniasis Case, treated with 15 doses of non-liposomal Amphotericin B on alternate days

value: Male


title: WB_exp1_EHC_Rep5

description:
Experiment 1
SAMPLE 30

value: Endemic Healthy Control (serology and quantiferon negative)

value: Female


title: 697-Combi-2

description: 697 cell line - DEXA+KPT treatment

value: RNA sequencing


title: WB_exp1_Quantiferon_Rep7

description:
Experiment 1
SAMPLE 27

value: Quantiferon positive asymptomatic


title: 697-Combi-1

description: 697 cell line - DEXA+KPT treatment


title: WB_exp1_ActiveCase_Patient8

description:
Experiment 1
SAMPLE 28

value: Active Visceral Leishmaniasis Case


title: SUPT1-DMSO-1

description: SUPT-1 cell line - DMSO treatment

value: DMSO


title: WB_exp1_ActiveCase_Patient7

description:
Experiment 1
SAMPLE 26


title: Donor_A_day_11 [A22.D11]

description: Humanized donor A, day 11 post 7 days of antibiotics

tag: tissue

value: Colon

tag: colonisation

value: Humanized germ free

value: 16 weeks

tag: day


title: Donor_B_day_11 [B22.D11]

description: Humanized donor B, day 11 post 7 days of antibiotics

tag: donor

value: B


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Thermus_thermophilus_ParB


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Streptomyces_coelicolor_ParB


title: Donor_A_day_11 [A21.D11]


title: WB_exp1_Treated_Patient6

description:
Experiment 1
SAMPLE 24


title: Donor_B_day_11 [B11.D11]


title: 697-KPT-2

description: 697 cell line - KPT treatment

tag: cell line

tag: protocol

tag: agent

value: KPT


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Staphylococcus_aureus_Noc

tag: genotype


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Staphylococcus_aureus_ParB


title: Donor_A_day_11 [A11.D11]


title: 697-KPT-1

description: 697 cell line - KPT treatment


title: Donor_B_day_11 [B21.D11]


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Sinorhizobium_meliloti_ParB


title: 697-KPT-3

description: 697 cell line - KPT treatment


title: WB_exp1_Treated_Patient7

description:
Experiment 1
SAMPLE 25


title: WB_exp1_Quantiferon_Rep6

description:
Experiment 1
SAMPLE 22


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Pseudomonas_aeruginosa_ParB


title: 697-DEX-2

description: 697 cell line - DEXA treatment

value: DEXA


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Porphyromonas_gingivalis_ParB


title: 697-DEX-1

description: 697 cell line - DEXA treatment


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Mycobacterium_tuberculosis_ParB


title: 697-DMSO-3

description: 697 cell line - DMSO treatment


title: Donor_A_day_11 [A12.D11]

value: A


title: WB_exp1_ActiveCase_Patient6

description:
Experiment 1
SAMPLE 23


title: WB_exp1_Treated_Patient5

description:
Experiment 1
SAMPLE 21


title: 697-DEX-3

description: 697 cell line - DEXA treatment


title: Donor_A_day_8 [A11.D8]

description: Humanized donor A, day 8 post 7 days of antibiotics


title: WB_exp1_Treated_Patient4

description:
Experiment 1
SAMPLE 16


title: 697-DMSO-2

description: 697 cell line - DMSO treatment


title: WB_exp1_ActiveCase_Patient5

description:
Experiment 1
SAMPLE 20


title: 697-DMSO-1

description: 697 cell line - DMSO treatment


title: WB_exp1_HighAb_Rep2

description:
Experiment 1
SAMPLE 17

value: High anti-leishmanial antibody levels by direct agglutination test


title: Donor_B_day_8 [B11.D8]

description: Humanized donor B, day 8 post 7 days of antibiotics


title: Donor_B_day_11 [B12.D11]


title: Donor_B_day_8 [B12.D8]


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Lactobacillus_aviarius_ParB

value: mixed population, exponential phase


title: WB_exp1_Quantiferon_Rep5

description:
Experiment 1
SAMPLE 18


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Lactobacillus_aviarius_Noc


title: WB_exp1_EHC_Rep4

description:
Experiment 1
SAMPLE 19


title: Donor_A_day_8 [A22.D8]


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Lawsonia_intracellularis_ParB


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Desulfovibrio_vulgaris_ParB


title: TR28_6KR_MOI10_III

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: TRIM28 6KR IAV infected

extract_protocol:
Total RNA from three independent replicates was extracted using the Reliaprep RNA cell kit (Promega) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: lung epithelial carcinoma

tag: infection

value: Influenza A/WSN/33, MOI10 PFU/cell, 6hpi

tag: genotype/variation

value: CRISPR/Cas9-edited TRIM28 KO lentivirally transduced with TRIM28 6KR mutant


title: WB_exp1_EHC_Rep3

description:
Experiment 1
SAMPLE 14

value: Endemic Healthy Control (serology and quantiferon negative)

value: Female


title: TR28_6KR_MOI10_II


title: Donor_B_day_8 [B21.D8]

value: Male


title: WB_exp1_ActiveCase_Patient4

description:
Experiment 1
SAMPLE 15

value: Active Visceral Leishmaniasis Case


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Dechloromonas_aromatica_ParB


title: TR28_6KR_MOI10_I


title: Donor_A_day_8 [A21.D8]


title: Donor_A_day_8 [A12.D8]


title: WB_exp1_Quantiferon_Rep4

description:
Experiment 1
SAMPLE 13

value: Quantiferon positive asymptomatic


title: Donor_B_day_8 [B22.D8]

value: Colon


title: TR28_6KR_mock_III

source_name: TRIM28 6KR mock

value: uninfected (mock)


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Clostridium_difficile_ParB


title: Donor_B_day_0 [B12.D0]

description: Humanized donor B baseline

value: Humanized germ free

value: 16 weeks


title: WB_exp1_Quantiferon_Rep3

description:
Experiment 1
SAMPLE 12


title: WB_exp1_EHC_Rep2

description:
Experiment 1
SAMPLE 11


title: TR28_6KR_mock_I


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Clostridium_difficile_Noc


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Caulobacter_crescentus_ParB


title: Donor_A_day_0 [A11.D0]

description: Humanized donor A baseline


title: Donor_A_day_0 [A22.D0]

description: Humanized donor A baseline


title: WB_exp1_Treated_Patient3

description:
Experiment 1
SAMPLE 10

value: Active Visceral Leishmaniasis Case, treated with 15 doses of non-liposomal Amphotericin B on alternate days


title: WB_exp1_HighAb_Rep1

description:
Experiment 1
SAMPLE 8


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Bifidobacterium_longum_ParB


title: hESC2.6 G12

city: Boston

first: Soohyun

last: Lee

state: MASSACHUSETTS

address: 10 Shattuck St.

department: Department of Biomedical Informatics

institute: Harvard Medical School

description: ESC

data_processing:
Alignment: Reads were aligned to a pre-digested genome with fragments between 28-300bp pafter MspI digestion, using maq with the following flags -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent*1000

growth_protocol: hESC lines and hiPSC lines were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. Medium containing DMEM/F12, 20% knockout serum replacement, 1mM L-glutamine, 100 uM MEM non-essential amino acids, and 0.1 mM beta-mercaptoethanol was used. 10 ng/ml of FGF-2 was added after sterile filtration and cells were fed daily and passaged weekly using 6 U/mL dispase or mechanically.

extract_protocol:
Undifferentiated hESC/hiPSC cells were sorted for hTRA-1-81+ to control for the homogeneity of cells before RNA extraction. The quality and quantity of total input mRNA was determined on an Agilent BioAnalyzer 2100 using Agilent RNA 6000 Nano kit. One microgram of total RNA from each sample was then used as input for library preparation using Illumina TruSeq RNA Sample Prep Kit, following manufacturerâ€™s instructions. Each paired-end library was prepared with an adaptor with unique index sequence. The size profile and quantity of resulting libraries were than determined on the BioAnalyzer 2100 with Agilent High Sensitivity DNA kit. These libraries were then pooled together at equal molar concentration and sequenced on an Illumina HiSeq 2000. All hESC and hiPSC samples for RNA-Seq analysis were prepared on the same day by the same person, and then sequenced simultaneously on the same run (except for hiPSC lines 1, 2 and 3; this did not affect the clustering). All fibroblasts samples were prepared and sequenced in the same manner as the pluripotent samples but on different days.
Libraries were created using the Nugen Ovation bisulfite kit.

treatment_protocol: Cells were harvested following acutase treatment and processed for DNA extraction

value: ESC


title: wt_TR28_MOI10_II

source_name: TRIM28 wt IAV infected

value: CRISPR/Cas9-edited TRIM28 KO lentivirally transduced with TRIM28 wt


title: WB_exp1_ActiveCase_Patient3

description:
Experiment 1
SAMPLE 9


title: Donor_B_day_0 [B22.D0]

description: Humanized donor B baseline

value: B


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Bacillus_subtilis_ParB

value: mixed population, exponential phase


title: wt_TR28_MOI10_III

value: lung epithelial carcinoma


title: hESC3.6 G2

description: ESC


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Bacillus_subtilis_Noc


title: WB_exp1_Quantiferon_Rep2

description:
Experiment 1
SAMPLE 7


title: Donor_B_day_0 [B21.D0]

description: Humanized donor B baseline


title: Donor_A_day_0 [A12.D0]

description: Humanized donor A baseline

value: A


title: hESC3.6 G3

description: ESC


title: LeLab_ChIPseq_TLE3000_pUT18C_1xFLAG_Agrobacterium_tumefaciens_ParB


title: hiPSC8

description: iPSC

value: iPSC


title: WB_exp1_Treated_Patient2

description:
Experiment 1
SAMPLE 6


title: wt_TR28_mock_III

source_name: TRIM28 wt mock


title: TR28_6KR_mock_II

value: CRISPR/Cas9-edited TRIM28 KO lentivirally transduced with TRIM28 6KR mutant


title: hiPSC3

description: iPSC


title: wt_TR28_MOI10_I

value: Influenza A/WSN/33, MOI10 PFU/cell, 6hpi


title: wt_TR28_mock_II


title: wt_TR28_mock_I


title: HUES3

description: ESC


title: hiPSC9

description: iPSC


title: A. terreus_240h

city: Bangkok

first: Pajareeya

last: Sogserm

address: 254 Chulalongkorn University Institute Building 3, Phayathai Road, Pathum Wan

department: The Institute of Biotechnology and Genetic Engineering

country: Thailand

institute: Chulalongkorn University

data_processing:
Sequencing was performed on the Ion Proton with the signal processing and basecalling using Ion Torrent Suite v5.0.4 (Life Technologies). Raw sequence from each sample was uploaded to Partek Flow.
Adapter sequences were trimmed. The sequence alignment with A. terreus NHI2624 (assembly ASM14961v1) genome was performed using STAR v2.4.2a.
Quantification of gene expression was done using Htseq (version0.6.0) with -f and -s options indicating bam inputs and un-stranded reads respectively
Cuffdiff (version 2.1.1) was used to estimate transcript abundance, by using the --no-diff option, and Ê with default options to generate differential analysis files for each of the described comparisons.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample and  the differential gene expression levels at the certain time.

organism: Aspergillus terreus

source_name: Fungal mycelia

growth_protocol: The fermentation was initiated by inoculating the fermentor with the spore suspension. During 48 h of the growth phase, the fermentor was operated at 30 °C, pH 3.0, 100 rpm, and 0.5 vvm air. After that, medium A was aseptically replaced by medium B. The operating conditions during the production phase was maintained at 30 °C and 100 rpm. The pH was automatically controlled at 2.0 by 5 M KOH. The DO was maintained at 10% by manipulating the aeration rate.

extract_protocol:
Fungal mycelia were homogenize and then RNA was extracted and centrifuged to pellet the RNA.
Barcoded RNA libraries were prepared using Lexogen’s Quant-Seq 3’ mRNA seq kit for Ion Torrent. This approach generated the libraries of the sequences close to the 3’ end of the polyadenylated RNAs and only one fragment was produced per transcript. The RNA input was quantified by the spectrophotometry or the fluorometry. Approximately 300-500 ng of the RNA input was required for the library generation. The modified Quant-Seq protocol was performed as suggested for the low input, partially degraded RNA. The External RNA Controls Consortium (ERCC) obtained from Life Technologies were used to spike into each of the prepared library reactions at the manufacturer’s recommended concentration. The library quantification and quality control were performed using high sensitivity DNA kit and Agilent 2100 Bioanalyzer.

tag: strain

value: NRRL 1960


title: WB_exp1_Quantiferon_Rep1

description:
Experiment 1
SAMPLE 3

value: Female


title: WB_exp1_ActiveCase_Patient2

description:
Experiment 1
SAMPLE 5

value: Active Visceral Leishmaniasis Case

value: Male


title: hESC2.6 G5

description: ESC

tag: cell type


title: A. terreus_216h


title: hESC2.6 Fib

description: Fibroblast

value: Fibroblast


title: WB_exp1_EHC_Rep1

description:
Experiment 1
SAMPLE 4

value: Endemic Healthy Control (serology and quantiferon negative)


title: A. terreus_144h


title: A. terreus_192h


title: WB_exp1_ActiveCase_Patient1

description:
Experiment 1
SAMPLE 1


title: WB_exp1_Treated_Patient1

description:
Experiment 1
SAMPLE 2


title: A. terreus_168h


title: Hep3B Knocked down for IGF2 Replicate 3

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v.3) in R.3.2.1

source_name: Hep3B Knocked down for IGF2

label_protocol: Standard Affymetrix protocol

growth_protocol: DMEM or RPMI supplemented with 10% FBS

extract_protocol: RNAeasy Mini Kit Qiagen

treatment_protocol: Lipofectamine transfection and antibiotic selection

value: Liver cell Line

value: IGF2 knockdown

tag: [igf2 group]

value: Low


title: A. terreus_120h


title: hESC3.6 Fib

description: Fibroblast


title: Hep3B Knocked down for IGF2 Replicate 2


title: Hep3B WT Replicate 3

source_name: Hep3B WT

value: wild type

value: High


title: SEB_ZT14

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

data_processing:
Adapter trimming was done using Universal adaptor sequences by Trimmomatic
The HQ reads so obtained were further processed as per Kallisto protocol (Bray et al., 2016)
Genome_build: De Novo
Supplementary_files_format_and_content: m8 file (tab separated)

organism: Emberiza melanocephala

source_name: Caught from wild

extract_protocol:
The total RNA extraction was done using Tri reagent (AM7020; Ambion, Austin, TX, USA).
RNA libraries were prepared for sequencing using standard Illumina sequencing protocols

tag: group

value: Sensitive Bunting (Blood collected at hour 14)

value: Blood

tag: time


title: SNU449 overexpressing IGF2 Replicate 3

source_name: SNU449 overexpressing IGF2

value: overexpressing IGF2


title: Hep3B Knocked down for IGF2 Replicate 1


title: SEB_ZT10

value: Sensitive Bunting (Blood collected at hour 10)


title: A. terreus_96h

tag: age


title: Hep3B WT Replicate 2


title: GEMM:RNA.32

description: GEMM overexpressing IGF2:RNA.32

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: Liver Tissue

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

growth_protocol: Hydrodynamic tail vein injection was the method selected to injected transposon plasmids and Sleeping Beauty transposase 13.

extract_protocol: tumor RNA was extracted using Qiagen RNeasy Mini (Qiagen, Germany).

treatment_protocol: no treatment

tag: [gemm group]


title: REB_ZT14

value: Refractory Bunting (Blood collected at hour 14)

tag: tissue


title: REB_ZT10

value: Refractory Bunting (Blood collected at hour 10)


title: GEMM:RNA.10

description: GEMM overexpressing IGF2:RNA.10


title: GEMM:RNA.28

description: GEMM overexpressing IGF2:RNA.28


title: SNU449 overexpressing IGF2 Replicate 2


title: A. terreus_72h

value: NRRL 1960


title: A. terreus_48h


title: GEMM:RNA.30

description: GEMM overexpressing IGF2:RNA.30


title: GEMM:RNA.22

description: GEMM overexpressing IGF2:RNA.22


title: GEMM:RNA.25

description: GEMM overexpressing IGF2:RNA.25


title: Hep3B WT Replicate 1


title: ETP-ALL4 (Hi-C)

status: Public on Aug 04 2019

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

description:
Primary T-ALL, classified as Early T Progenitor (ETP) subtype based on transcriptomic profiling. Enzymatic restriction was peformed using commercial Arima kit.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

data_processing:
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the hg19 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<25 kb)
Matrix generation: HicBench. For each sample and each chromosome, a matrix with binned interactions (bin-size 40kb) was generated.
Normalization: ICE normalization as described in Imakaev et al. (2012) was employed first. We then applied normalization by distance as recently described (Gong et al., 2018)
Topologically Associated Domains (TAD) calls: TADs were called using the algorithm developed within hic-bench, setting the insulating window to 500kb.
Genome_build: hg19
Supplementary_files_format_and_content: TAD bed files, scores.tsv files

source_name: Peripheral blood primary T-ALL cells

growth_protocol: CUTLL1 and Jurkat cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, T-ALL cells were isolated from spleen by flow cytometer using hCD45 as marker;  Healthy T cells were purchased from Lonza (catalog no: 2W-200)

extract_protocol:
Nuclear extraction and DNA purification using Amicon Ultra 30K
End-repair was performed using T4 DNA polymerase (NEB), T4 DNA polynucleotide kinase (NEB), Klenow (NEB) and dNTPs in 1× T4 DNA ligase reaction buffer (NEB), followed by dATP-addition with Klenow. Paired-end (PE) adapters (Illumina) were ligated to DNA fragments using 15 U of the T4 DNA ligase (Invitrogen) for 2 hours at room temperature. Bead-bound DNA was amplified with 6 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). Library prepartion of samples prcoessed using Arima HiC kit were prepared using Kap Hper library prep kit (KK8504)as per manufacturer's guidelines.

treatment_protocol: CUTLL1 cells were treated with DMSO or gamma-secretase inhibitor (1 uM) for 72 hours or THZ1 (100 nM) for 24 hours.

value: Peripheral blood

value: primary T-ALL cells

tag: disease state

value: Primary T-ALL

tag: treatment

tag: enzymatic restriction

value: commercial Arima kit


title: CUTLL1 gSI input (ChIP-seq)

data_processing:
Read alignment: Reads were aligned against the reference sequence hg19 with bowtie2 (version 2.3.1) with standard parameters and only uniquely mapped reads were kept with MAPQ > 20.
Deduplication: Aligned reads were filtered for duplicated reads using picard-tools version 2.6.0.
Peak-calling: Peak calling for CTCF and H3K27ac was performed using MACS2 (version 2.0.1) using narrow (CTCF) and broad (--broad; H3K27ac) option (sepcial parameters: --no-model).
Differential binding: To identify differentially bound peaks, we performed diffBind (version 2.2.12) analysis, using the normalization option DBA_EDGER.
Bigwig: For visualization purposes, we generated fold-enrichment bigwig files by applying MACS2 (version 2.0.1) bdgcmp over input (-m FE)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, peak (bed)

source_name: T-ALL Cell line

growth_protocol: CUTLL1 cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, and when the tumor bueden in pheripheral blood reached 80%, the mice were sacrificed and the spleen was harvested and splenocytes were used for the Chip-Seq analysis;  Healthy T cells were purchased from Lonza (catlog no: 2W-200)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
libraries were prepared using Kapa Hyper prep kit (Catalog no: KK8500) following manufacturer's guidelines

treatment_protocol: CUTLL1 cells were treated with gamma-secretase inhibitor (1 uM) for 72 hours or BET inhibitor (JQ1, 500 nM) for 24h or CDK7 inhibitor (THZ1, 100 mM) for 24 hours.

tag: cell line

value: T-ALL

value: gSI (1uM)

tag: chip antibody


title: SNU449 WT Replicate 2

source_name: SNU449 WT

value: Liver cell Line


title: GEMM:RNA.5

description: GEMM control:RNA.5


title: CUTLL1 gSI CTCF rep3 (ChIP-seq)

description:
CUTLL1_gSI_CTCF_narrow-peaks.bed
CUTLL1_gSI_CTCF_FE.bw

value: CTCF (D31H2; Catalog no:3418)


title: ETP-ALL3 (Hi-C)


title: CUTLL1 gSI CTCF rep1 (ChIP-seq)


title: GEMM:RNA.4

description: GEMM control:RNA.4


title: mouse11_m_early adversity_1_rep1

city: Bordeaux

first: Muriel

last: DARNAUDERY

address: rue leo saignat

department: INRA

institute: bordeaux university

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min). Two washing procedures were sequentially performed to achieve the wash of 6 slides (3 slides each).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 38 out of 47 microarrays or with a minimal weight of 8 per group from at least one experimental group. At this step, 39656 spots out of 62976 were selected.  The mean signal of the 24 first samples and 23 last ones were substracted to individuals signals to correct the batch effect of the 2 serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36975 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: medial prefrontal cortex

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA extraction protocol not provided.

tag: technical replicate

tag: batch

value: medial prefrontal cortex

tag: gender

value: M

value: early adversity


title: CUTLL1 H3K27ac (HiChIP)

data_processing:
Library strategy: HiChIP
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the mm10 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<10 kb)
Matrix generation: HicBench. For each replicate and each chromosome, a matrix with binned interactions (bin-size 10kb) was generated.
Normalization: custom script. Each loop with > 1 read was kept. We applied normalization by sequencing depth to raw read-counts (leading to counts-per-million; CPM).
High-confidence interactions: custom script. We have applied an approach similar to mango, which employs a binomial test per diagnoal in the normalized counts-matrix. To define significant HiChIP loops, we have filtered all interactions for CPM>5 and FDR<0.1.
Genome_build: hg19
Supplementary_files_format_and_content: TSV - significant loops

growth_protocol: CUTLL1 cells were grown in RPMI medium with 10% FBS

extract_protocol:
Nuclear extraction and DNA purification using Amicon Ultra 30K
Libraries prepared using Kapa Hper Library prep kits (KK8504) as per manufacturer's guidelines.

value: H3K27ac (Active motif; Catalog no:39133)


title: ETP-ALL2 (Hi-C)


title: SNU449 WT Replicate 1

description: 1_SNU449_Empty_1 _A05.CEL

tag: genotype/variation

value: wild type

value: Low


title: mouse25_f_early adversity_2_rep1

tag: strain

value: F


title: SNU449 overexpressing IGF2 Replicate 1

tag: cell type

value: overexpressing IGF2

value: High


title: CUTLL1 CTCF rep5 (ChIP-seq)

description:
CUTLL1_DMSO_CTCF_narrow-peaks.bed
CUTLL1_DMSO_CTCF_FE.bw

value: DMSO


title: mouse44_f_control_3_rep1

value: control


title: CUTLL1 CTCF rep4 (ChIP-seq)


title: mouse7_m_early adversity_1_rep2


title: CUTLL1 input (ChIP-seq)


title: SNU449 WT Replicate 3

tag: [igf2 group]


title: mouse8_m_control_1_rep2


title: CUTLL1 CTCF rep3 (ChIP-seq)


title: mouse39_f_early adversity_3_rep1


title: mouse32_f_control_2_rep1


title: mouse27_f_early adversity_2_rep1


title: mouse7_m_early adversity_1_rep1


title: mouse14_m_control_1_rep1


title: CUTLL1 CTCF rep2 (ChIP-seq)


title: GEMM:RNA.6

description: GEMM control:RNA.6


title: mouse46_f_early adversity_3_rep1


title: mouse10_m_control_1_rep1


title: mouse9_m_early adversity_1_rep1


title: CUTLL1 CTCF rep1 (ChIP-seq)


title: CUTLL1 gSI rep2 (Hi-C)

description:
CUTLL1 cell line model for T-ALL, treated with NOTCH-inhibitor gamma-secretase inhibitor (gSI). Enzymatic restriction was peformed using HindIII.
CUTLL1_gSI_TADs_hicratio-500kb-activity.bed
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

value: HindIII


title: Jurkat DMSO rep1 (Hi-C)

description:
Jurkat cell line model for T-ALL. Enzymatic restriction was peformed using HindIII.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

value: Jurkat


title: mouse23_m_early adversity_2_rep1


title: CUTLL1 gSI rep1 (Hi-C)

value: T-ALL


title: CUTLL1 DMSO HindIII rep2 (Hi-C)

description:
CUTLL1 cell line model for T-ALL. Enzymatic restriction was peformed using HindIII.
CUTLL1_DMSO_HindIII_TADs_hicratio-500kb-activity.bed
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv


title: ETP-ALL4 (RNA-seq)

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM table

growth_protocol: Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft and when the tumor bueden in pheripheral blood reached 80% the mice were the spleen was harvested and splenocytes were used for the RNA-Seq analysis.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit using Qiagen kit (Catalog no: 74106) folllowing manufacturer's guidelines.
The libraries were prepared using NEXTflex Rapid Directional RNA-Seq Kit from Bioo Scientific (Catalog no: 5138-07) folllowing manufacturer's guidelines.

value: Peripheral blood

value: primary T-ALL cells

value: T cell acute lymphoblastic leukemia


title: Tcell1 (Hi-C)

description:
Healthy T cells purchased from Lonza (catalog no: 2W-200). Enzymatic restriction was peformed using HindIII.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

source_name: Peripheral blood T cells

value: T cells

value: Healthy T cells


title: Tcell2 (Hi-C)


title: mouse3_m_early adversity_1_rep1

value: medial prefrontal cortex

value: M

value: early adversity


title: mouse29_f_early adversity_2_rep1


title: ETP-ALL1 (RNA-seq)


title: mouse4_m_control_1_rep1


title: mouse38_f_control_3_rep1


title: CUTLL1 gSI H3K27ac rep2 (ChIP-seq)

description:
CUTLL1_gSI_H3K27ac_broad-peaks.bed
CUTLL1_gSI_H3K27ac_FE.bw

value: gSI (1uM)

value: H3K27ac (Active motif; Catalog no:39133)


title: CUTLL1 gSI H3K27ac rep1 (ChIP-seq)


title: mouse30_f_control_2_rep1

value: F


title: mouse21_m_early adversity_2_rep1


title: mouse6_m_control_1_rep1


title: mouse42_f_control_3_rep1


title: mouse16_m_control_1_rep1


title: mouse28_f_control_2_rep1


title: CUTLL1 DMSO HindIII rep1 (Hi-C)


title: mouse15_m_early adversity_1_rep1


title: mouse17_m_early adversity_2_rep1


title: mouse33_f_early adversity_3_rep1


title: mouse8_m_control_1_rep1


title: mouse43_f_early adversity_3_rep1


title: mouse12_m_control_1_rep1


title: mouse35_f_early adversity_3_rep1


title: mouse36_f_control_3_rep1


title: T cell CTCF rep2 (ChIP-seq)

description:
Tcells_CTCF_narrow-peaks.bed
Tcells_CTCF_FE.bw

value: CTCF (D31H2; Catalog no:3418)


title: CUTLL1 H3K27ac rep2 (ChIP-seq)

description:
CUTLL1_DMSO_H3K27ac_broad-peaks.bed
CUTLL1_DMSO_H3K27ac_FE.bw

value: DMSO


title: CUTLL1 H3K27ac rep1 (ChIP-seq)


title: T cell input (ChIP-seq)

source_name: Pheripheral blood T cells


title: hiPSC1

description: iPSC

value: iPSC


title: T cell CTCF rep1 (ChIP-seq)


title: mouse45_f_early adversity_3_rep1


title: mouse24_f_control_2_rep1

value: control


title: mouse13_m_early adversity_1_rep1


title: mouse5_m_early adversity_1_rep1


title: mouse37_f_early adversity_3_rep1


title: mouse22_m_control_2_rep1


title: CUTLL1 10h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
10h_2
10h_forward.bw
10h_reverse.bw

data_processing:
library strategy: GRO-seq
Read alignment: Reads were aligned against hg19 using bowtie with standard parameters. Only uniquely mapped reads with MAPQ > 20 were kept.
Read counting: All remaining aligned reads were counted in a stranded-manner on a gene-basis for all annotated genes in Ensembl Genes V75 using bamutils count of the ngsutils package (version 0.5.7). Specific options were -uniq -multiple complete -library RF.
Normalization: Read counts were normalized with edgeR (version 3.14.0; functions calcNormFactors and estimateTagwiseDisp). FPKM normalization was applied with edgeR using CDS length downloaded from Ensembl Genes V75.
Visualization: Aligned sequencing reads were used to generate bigwig tracks per genomic strand using bedtools (version 2.27.1; options -fs 250) after normalizing for sequencing depth and fragment length.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, FPKM tsv

molecule: nuclear RNA

source_name: T-ALL cell line

growth_protocol: CUTLL1 cells were grown in RPMI medium with 10% FBS.

extract_protocol:
Trizol, phenol/chloroform
TruSeq Small RNA Library Preparation Kit was used as by manufacturers instructions.

treatment_protocol: CUTLL1 cells were treated with gamma-secretase inhibitor (1 uM) for 72 hours, and followed after release of the drug for 10 hours.

value: gSI (1uM)  for 72h

tag: drug release


title: mouse31_f_early adversity_2_rep1


title: Jurkat input (ChIP-seq)

value: Jurkat

value: T-ALL


title: Jurkat CTCF rep2 (ChIP-seq)

description:
Jurkat_CTCF_narrow-peaks.bed
Jurkat_CTCF_FE.bw


title: CUTLL1 10h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
10h_1
10h_forward.bw
10h_reverse.bw


title: Jurkat CTCF rep1 (ChIP-seq)


title: mouse20_m_control_2_rep1


title: mouse34_f_control_3_rep1


title: CUTLL1 08h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
08h_1
08h_forward.bw
08h_reverse.bw


title: MDA-MB468 Atorvastatin RNASeq

city: Sacramento

first: Demin

last: Cai

state: CA

institute: UC Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 sequencer.
The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Sequence reads were mapped to GRCh37/hg19 assembly with BWA and Biotie software.
The Cufflinks package was used for transcripts assembly, quantification of normalized gene and isoform expression, and analysis of different expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: TNBC cells

growth_protocol: HCC70 cells were cultured in RPMI supplemented with 10% FBS for maintenance for experiments. MDA-MB468 cells were cultured in RPMI supplemented with 10% FBS plus 1% insulin for maintenance for experiments. Cells were grown at 37℃ in 5% CO2 incubators.

extract_protocol:
1 μg of total RNA was extracted for each sample.
Libraries were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: HCC70 and MDA-MB468 cells were seeded into 6-well plates and cultured in growth medium. Next day, cell were treated with vehicle, XY018 (1.25 or 2.5 µM), atorvastatin (ATV, 1.25 µM) or the combination of XY018 (1.25 µM) and ATV for 24 hours. For MDA-MB468, cells were treated with vehicle or GSK805 (2.5 µM) for 24 hours before RNA extraction.

tag: passages


title: CUTLL1 06h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
06h_1
06h_forward.bw
06h_reverse.bw


title: CUTLL1 06h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
06h_2
06h_forward.bw
06h_reverse.bw


title: CUTLL1 05h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
05h_2
05h_forward.bw
05h_reverse.bw


title: CUTLL1 08h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
08h_2
08h_forward.bw
08h_reverse.bw


title: CUTLL1 05h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
05h_1
05h_forward.bw
05h_reverse.bw


title: mouse19_m_early adversity_2_rep1


title: MDA-MB468 Vehicle (for GSK805) RNASeq

description: MDA-MB468 GSK805 2.5.txt

value: Vehicle (for GSK805)


title: mouse26_f_control_2_rep1


title: mouse2_m_control_1_rep1


title: MDA-MB468 XY018_1.25µM combined with Atorvastatin RNASeq

description: MDA-MB468 combination cell.txt

value: XY018_1.25uM combined with Atorvastatin


title: MDA-MB468 GSK805_2.5µM RNASeq

description: MDA-MB468 GSK805 2.5.txt


title: mouse41_f_early adversity_3_rep1


title: mouse18_m_control_2_rep1


title: MDA-MB468 XY018_1.25µM RNASeq

description: MDA-MB468 combination cell.txt


title: CUTLL1 04h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
04h_2
04h_forward.bw
04h_reverse.bw


title: MDA-MB468 Vehicle (for combination) RNASeq

description: MDA-MB468 combination cell.txt

value: Vehicle (for combination)


title: HCC70 XY018_1.25µM combined with Atorvastatin_1.25µM RNASeq

description: HCC70 cell.txt

value: XY018_1.25uM combined with Atorvastatin_1.25uM


title: CUTLL1 04h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
04h_1
04h_forward.bw
04h_reverse.bw


title: CUTLL1 03h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
03h_1
03h_forward.bw
03h_reverse.bw


title: CUTLL1 02h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
02h_2
02h_forward.bw
02h_reverse.bw


title: HCC70 Atorvastatin_1.25µM RNASeq

description: HCC70 cell.txt


title: HCC70 XY018_2.5µM RNASeq

description: HCC70 cell.txt


title: CUTLL1 02h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
02h_1
02h_forward.bw
02h_reverse.bw


title: CUTLL1 01h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
01h_2
01h_forward.bw
01h_reverse.bw


title: HCC70 Vehicle RNASeq

description: HCC70 cell.txt

value: Vehicle


title: HCC70 XY018_1.25µM RNASeq

description: HCC70 cell.txt


title: CUTLL1 00h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
00h_2
00h_forward.bw
00h_reverse.bw


title: S9-jian

city: Shanghai

first: jingmin

last: Guan

address: 320 Yue Yang Road

department: Institute of Biochemistry and Cell Biolog

country: China

institute: Shanghai Institutes for Biological Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 0.12.8.
peaks were called using MACS version 1.4.2 and Different peaks were caculated by DiffBind in R with the Fold change >=2 and p value <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: peaks files were generated by MACS version 1.4.2 20120305. Fold_enrichment reprensent fold change. Fold change >=2 and p value <0.05.

source_name: mouse peritoneal macrophages

growth_protocol: The thioglycollate broth-induced peritoneal macrophages are harvested and they are cultured in dishes. When they become adherent and are treated with LPS or PBS for 24 h.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to standard Illumina protocols.

treatment_protocol: The adherent macrophages were treated with PBS or LPS for 24 h.

value: thioglycollate broth induced peritoneal macrophages

tag: age

value: 8 weeks

value: H3K9me3 (abcam, ab8898)

value: PBS treat 24 h


title: CUTLL1 01h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
01h_1
01h_forward.bw
01h_reverse.bw


title: MDA-MB468 XY018_2.5µM RNASeq

description: MDA-MB468 combination cell.txt


title: CUTLL1 03h rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
03h_2
03h_forward.bw
03h_reverse.bw


title: CUTLL1 00h rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
00h_1
00h_forward.bw
00h_reverse.bw


title: S4jia

value: H3K4me3 (abcam, ab8580)

value: LPS treat 24 h


title: S4-jian


title: CUTLL1 DMSO rep1 (GRO-seq)

description:
GROseq_FPKM_table.tsv
DMSO_1
DMSO_forward.bw
DMSO_reverse.bw

value: DMSO


title: NIL-Pigm

first: yiwen

last: Deng

state: Shanghai

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: treatment with blast isolate TH12

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the rice reference genome Nipponbare genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules
Supplementary_files_format_and_content: tab-delimited text files includeFPKM values for each Sample

organism: Oryza sativa

source_name: two-weeks seedling plants

growth_protocol: The RNA samples were isolated from the shoots of the variety NIL-Pigm and PIP1-RNAi grown in soil under 12-h-light/12-h-dark at 28°C in a greenhouse for 14 days, treatment with blast isolate TH12.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: seedling

value: WT

value: blast isolate TH12

value: leaf


title: S9jia


title: Corpus luteum, P2

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

data_processing:
All data processing was according to standard Beijing Genomics Institute protocols.
Raw reads were obtained and subjected to a quality control analysis, to determine if resequencing was needed.
High quality reads were then filtered from the entire set of raw reads for alignment.
Clean reads were aligned using Short Oligonucleotide Analysis Package (SOAP)2/SOAP aligner
Following alignment, an additional quality control step was included to determine if resequencing was needed, coverage analysis was performed, and distribution of reads of reference genes was assessed.
Genome_build: University of Maryland Bos taurus assembly 3.1
Supplementary_files_format_and_content: raw counts

organism: Bos taurus

source_name: Bovine corpus luteum

growth_protocol: none. This is a whole animal study

extract_protocol:
For next generation sequencing (NGS), total RNA was isolated from all 8 samples using the mirVana RNA isolation kit (ThermoFisher). RNA quantity and quality were assessed using a BioRad Experion and all samples had an RNA quality index (RQI) > 9.
Strand-specific sequencing was performed according to standard protocols at BGI. The library was constructed using 200 bp inserts of cDNA and library quality control was performed by qPCR, using an Agilent 2100 machine.

treatment_protocol: Half of the animals were bred and half were not bred.

tag: status of cow

value: day 17 pregnant

tag: tissue

value: Corpus luteum


title: Corpus luteum, P1


title: PIP1-GFP_ChIP

description: treatment with blast isolate TH12

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Nipponbare genome assembly using SOAPaligner/soap2. Clean Parameter: SOAPnuke1.5.0 filter-l 20 -q 0.5 -n 0.1-i-c 25 -Q 2
peaks were called using MACS (Model-based Analysis of ChIP -Seq) with the following setting: macs14-s 49-g380000000-p1e-5-w --space50-m 10,30.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: The DNA samples were isolated from the shoots of the transgenic plants containing PIP1-GFP grown in soil under 12-h-light/12-h-dark at 28°C in a greenhouse for 14 days

extract_protocol:
DNA was extracted with Dr.GenTLETM precipitation carrier (Takara), followed by clean-up and treatment with RNAase in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The two-weeks rice seedling were treated by blast isolat TH12, and collect the sample in 36 hours after treatment.

value: PIP1-GFP tansgenic

value: 2 week old seedling

tag: treatment

tag: antibody

value: GFP

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: variety background

value: NIL-Pigm


title: Corpus luteum, C2

value: day 17 cyclic


title: Corpus luteum, P5


title: Input_RORgamma_XY018_ChIPSeq

data_processing:
Sequencing tags were mapped against the Homo sapiens (Human) reference genome (hg19) using Bowtie 2.
Uniquely mapped tags were used for peak calling by MACS(2.1.0) to identify regions of ChIP-Seq enrichment over background.
A q value threshold of enrichment of 5 x 10^-2 was used for all data sets. by using ngs.plot (https://github.com/shenlab-sinai/ngsplot)
Normalized genome-wide signal coverage tracks from raw read alignment files were built by MACS2, fold-enrichment normalized wiggle files were generated by MACS by comparing ChIP treatment against input control, UCSC tools (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig/bedClip) and bedTools (http://code.google.com/p/bedtools/).
Visualization of ChIP-seq singnal at enriched genomic regions(avgprof and heatmap) was achieved
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using MACS2 and UCSC tools

source_name: triple-negative breast cancer cells

growth_protocol: HCC70 cells were cultured in RPMI supplemented with 10% FBS for maintenance for experiments. Cells were grown at 37℃ in 5% CO2 incubators.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's paired-end DNA sample Prep kit.

treatment_protocol: HCC70 cells were seeded into15 cm dish and cultured in RPMI supplemented with 10% FBS, next day, cell were then treated with vehicle or XY018 (5µM) for another 24 hours.

tag: cell line

tag: chip antibody


title: Corpus luteum, C4


title: Corpus luteum, C1


title: Corpus luteum, C3


title: IP_RORγ_XY018_ChIPSeq

value: anti-RORγ rabbit serum was generated by Covance, using purified GST-human RORγ fragment (amino acids 79-301) expressed in Escherichia coli.


title: PIP1-RNAi

description: treatment with blast isolate TH12

tag: genotype/variation


title: Input_RORgamma_Vehicle_ChIPSeq

value: vehicle


title: IP_RORgamma_Vehicle_ChIPSeq


title: CUTLL1 DMSO rep2 (GRO-seq)

description:
GROseq_FPKM_table.tsv
DMSO_2
DMSO_forward.bw
DMSO_reverse.bw


title: IL4_5

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
The raw reads in fastq format have been aligned to the mouse mm10 genome with Bowtie2/Tophat2 on the combined reference transcriptome from Ensembl 75 and UCSC mm10.
The identified transcripts are further assembled and analyzed for differential analysis with the pipeline Cufflinks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_transcripts.gtf: GTF files include FPKMs.

source_name: BMDM

growth_protocol: Bone marrow, isolated from femur, tibia and humerus was differentiated for 6 days on petri dishes. Differentiation medium consisted of DMEM high glucose (Gibco), 10% low endotoxin FBS (Gibco), 2 mM L-glutamine (Lonza), 100 U/ml penicillin (Sigma), 100 μg/ml streptomycin (Sigma), 50 μg/ml β-mercaptoethanol (Gibco) supplemented with either 15 ng/ml CSF1 (Peprotech) or 10–20 % L929 conditioned supernatant. Three days later, non-adherent cells were removed and cells were split 1:2 in fresh medium. On day 6, differentiated BMDM (96% of the cells were positive for F4/80 and CD11b) were washed, dislocated gently with a cell scraper, and seeded in the indicated medium.

extract_protocol:
Qiagen RNeasy Plus Micro Kit was used to isolate total RNA according to manufacturer's instructions. Quality control of RNA samples was performed using RNA 6000 Nano Kit on an 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared at the Core facility Genomics, Medical University of Vienna using the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina according to manufacturer’s protocols (New England Biolabs). Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantitated using Qubit dsDNA HS Assay (Invitrogen).
Pooled libraries had an average length of 330-360bp and were sequenced on a NextSeq500 instrument (Illumina) in 1 x 75 bp sequencing mode.

treatment_protocol: Differentiated BMDMs were seeded in DMEM high glucose (Gibco), 10% low endotoxin FBS (Gibco), 2 mM L-glutamine (Lonza), 100 U/ml penicillin (Sigma), 100 μg/ml streptomycin (Sigma), 50 μg/ml β-mercaptoethanol (Gibco) over night. The next morning, they were pre-treated with 30 µM of the PHGDH inhibitor CBR-5884 (AxonMedchem) or solvent. Thereafter, 10 ng/ml IL-4 (Peprotech) was added and cells were harvested 24h later.

tag: strain/background

value: wild type

value: bone marrow-derived macrophages


title: Input_SREBP2_XY018_ChIPSeq


title: Corpus luteum, P4


title: Input_SREBP2_Vehicle_ChIPSeq


title: IP_SREBP2_XY018_ChIPSeq


title: CUTLL1 gSI CTCF rep2 (ChIP-seq)

description:
CUTLL1_gSI_CTCF_narrow-peaks.bed
CUTLL1_gSI_CTCF_FE.bw

tag: disease state

value: T-ALL

value: gSI (1uM)

value: CTCF (D31H2; Catalog no:3418)


title: Input_H3K27ac_XY108_ChIPSeq


title: Input_H3K27ac_Vehicle_ChIPSeq


title: CBR_5

tag: cell type


title: CBR_4


title: IP_SREBP2_Vehicle_ChIPSeq


title: IP_H3K27ac_Vehicle_ChIPSeq

value: H3(acetyl K27) (Abcam; ab4729)


title: CBR_3


title: CUTLL1 THZ1 Arima rep2 (Hi-C)

description:
CUTLL1 cell line model for T-ALL, treated with CDK7-inhibitor THZ1. Enzymatic restriction was peformed using commercial Arima kit.
CUTLL1_THZ1_Arima_TADs_hicratio-500kb-activity.bed
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

tag: enzymatic restriction

value: commercial Arima kit


title: ETP-ALL3 (RNA-seq)

value: Peripheral blood

value: primary T-ALL cells

value: T cell acute lymphoblastic leukemia


title: CUTLL1 THZ1 Arima rep1 (Hi-C)


title: IL4_3


title: ETP-ALL2 (RNA-seq)


title: CUTLL1 DMSO Arima rep2 (Hi-C)

description:
CUTLL1 cell line model for T-ALL. Enzymatic restriction was peformed using commercial Arima kit.
CUTLL1_DMSO_Arima_TADs_hicratio-500kb-activity.bed
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

value: DMSO


title: IP_H3K27ac_XY018_ChIPSeq

tag: passages


title: K562 CALRins5 Melittin replicate 3

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description: K562 transduced with CALRins5 and treated with Melittin replicate 3

hyb_protocol: The hybridization, staining and scanning of HG U133_Plus 2 GeneChip (Affymetrix; Santa Clara, CA) were performed by using Hybridization, Wash, and Stain Kit for 3’IVT Arrays and Affymetrix standard protocols (Affymetrix, Santa Clara, CA, USA). In particular, fragmented cRNA was hybridized for 16 hr at 45°C on Affymetrix HG U133_Plus 2 GeneChip and GeneChip Hybridization Oven 645. GeneChips were washed and stained using Affymetrix GeneChip® Fluidics Station 450 according to the standard protocol supplied by Affymetrix.

scan_protocol: Affymetrix HG U133_Plus 2 GeneChip were finally scanned using Affymetrix® GeneChip® Scanner 3000.

data_processing: The probe signal data were normalized and converted into expression values using the robust multiarray average (RMA) procedure. Quality control was assessed by using QC procedures included in the Partek GS. 6.6 Software Package (http://www.partek.com).

source_name: K562 cells

label_protocol: GEP was performed on RNA samples isolated from wt, CALRdel52 and CALRins5 K562 cells immediately after NGFR-based sorting from 3 independent experiments. As far as GEP upon Melittin exposure is concerned, RNA samples were isolated from wt, CALRdel52 and CALRins5 K562 after 24h of Melittin 5μg/mL treatment.GEP cDNA synthesis and biotin-labeled target synthesis were performed using the GeneChip 3' IVT Plus Reagent Kit according to the protocol supplied by Affymetrix.

growth_protocol: K562 cells were seeded at 3×10^5 cells/mL in RPMI-1640 medium (Euroclone) supplemented with 10% FBS (Sigma-Aldrich). Subsequent passages were performed when cells reached 60–80% confluency.

extract_protocol: Total cellular RNA was harvested from 1×105 cells from each sample using the miRNeasy Micro RNA isolation kit (QIAGEN), according to the manufacturer’s instructions. RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).

treatment_protocol: To induce oxidative stress, K562 cells were seeded at 5x10^5 cells/mL in RPMI-1640 supplemented with 10% FBS and exposed to Melittin 5 μg/mL (Sigma-Aldrich) for 24 hours at 37°C in a humidified atmosphere with 5% CO2.

tag: retroviral vector

value: LCALRins5IDN (CALRins5)

tag: agent

value: Melittin (MEL, 5ug/ml)

tag: replicate

value: K562 Cell line, from human blood(chronic myelogenous leukemia)


title: K562 CALR wild-type Untreated replicate 3

description: K562 transduced with CALR wild-type and Untreated replicate 3

value: LCALRwtIDN (CALR wild-type, CALRwt)

value: Untreated


title: CUTLL1 THZ1 H3K27ac rep2 (ChIP-seq)

description:
CUTLL1_THZ1_H3K27ac_broad-peaks.bed
CUTLL1_THZ1_H3K27ac_FE.bw

value: H3K27ac (Active motif; Catalog no:39133)


title: CUTLL1 THZ1 H3K27ac rep1 (ChIP-seq)


title: K562 CALRins5 Untreated replicate 3

description: K562 transduced with CALRins5 and Untreated replicate 3


title: K562 CALRdel52 Untreated replicate 3

description: K562 transduced with CALRdel52 and Untreated replicate 3

value: LCALRdel52IDN (CALRdel52)


title: K562 CALR wild-type Melittin replicate 3

description: K562 transduced with CALR wild-type and treated with Melittin replicate 3


title: K562 CALRdel52 Untreated replicate 2

description: K562 transduced with CALRdel52 and Untreated replicate 2


title: K562 CALRins5 Melitin replicate 2

description: K562 transduced with CALRins5 and treated with Melitin replicate 2


title: CALR INS clone C61

description: K562 cells transduced with LCALRins5IDN

hyb_protocol: The HG-U219 Array Strips (Affymetrix; Santa Clara, CA) hybridization, staining and scanning were performed by using the GeneAtlas Platform.

source_name: K562 cell line

label_protocol: GEP was performed on RNA samples isolated from wt, CALRdel52 and CALRins5 K562 cells immediately after NGFR-based sorting from 3 independent experiments.   GEP cDNA synthesis and biotin-labeled target synthesis were performed using the GeneAtlas 3´ IVT Express Kit according to the protocol supplied by Affymetrix.

growth_protocol: K562 cells were seeded at 3×105 cells/mL in Roswell Park Memorial Institute medium (RPMI-1640; Euroclone) supplemented with 10% FBS (Sigma-Aldrich). Subsequent passages were performed when cells reached 60–80% confluency

treatment_protocol: The cDNAs coding for human CALR (NM_004343) and the two commonest CALR mutated variants (CALRdel52/type I and CALRins5/type II) were synthesized (service from OriGene Technologies, Inc. USA) and cloned into retroviral vector LXIDN (Ruberti et al., 2017). Packaging line for LCALRwtIDN, LCALRdel52IDN, LCALRins5IDN were generated by transnfection in the ecotropic Phoenix and amphotropic GP+envAm12 cells, as previously described (Ruberti et al., 2017). Transduction of K562 cells was performed by four cycles of infection (one every 12h) with viral supernatant with the addition of polybrene (8 μg/ml), and 20% FBS (Sigma-Aldrich) in retronectin-coated plates.After transduction, K562 cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640; Euroclone) supplemented with 20% FBS for additional 36h. Transduced K562 cells were subsequently purified by means of immunomagnetic selection (EasySep “Do-It-Yourself” Selection Kit; StemCell Technologies) using the anti-human p75-NGFR mouse monoclonal antibody (BD Biosciences). Purity of the NGFR+ cell fraction was assessed by flow cytometry after labeling with PE-conjugated anti-NGFR monoclonal antibody (Miltenyi) 48h post-purification and was always >90%.

tag: clone

value: clone 61


title: ETP-ALL1 (Hi-C)

description:
Primary T-ALL, classified as Early T Progenitor (ETP) subtype based on transcriptomic profiling. Enzymatic restriction was peformed using commercial Arima kit.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

tag: tissue

value: Primary T-ALL

tag: treatment


title: CUTLL1 H3K27ac rep4 (ChIP-seq)

description:
CUTLL1_DMSO_H3K27ac_broad-peaks.bed
CUTLL1_DMSO_H3K27ac_FE.bw

value: T-ALL


title: K562 CALRdel52 Melittin replicate 3

description: K562 transduced with CALRdel52 and treated with Melittin replicate 3


title: CALR DEL clone C61

description: K562 cells transduced with LCALRdel52IDN

scan_protocol: The HG-U219 Array Strips (Affymetrix; Santa Clara, CA) hybridization, staining and scanning were performed by using the GeneAtlas Platform.


title: K562 CALRins5 Untreated replicate 2

description: K562 transduced with CALRins5 and Untreated replicate 2


title: K562 CALR wild-type Melittin replicate 2

description: K562 transduced with CALR wild-type and treated with Melittin replicate 2


title: K562 CALR wild-type Untreated replicate 2

description: K562 transduced with CALR wild-type and Untreated replicate 2


title: CUTLL1 H3K27ac rep3 (ChIP-seq)


title: K562 CALR wild-type Untreated 1

description: K562 transduced with CALR wild-type and Untreated 1


title: Tcell3 (Hi-C)

description:
Healthy T cells purchased from Lonza (catalog no: 2W-200). Enzymatic restriction was peformed using commercial Arima kit.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv

value: T cells

value: Healthy T cells


title: CALR DEL clone C51

value: clone 51


title: CALR WT clone C51

description: K562 cells transduced with LCALRwtIDN

value: CALR wild-type, CALRwt


title: CALR WT clone C61

description: K562 cells transduced with LCALRwtIDN


title: K562 CALRins5 Untreated replicate 1

description: K562 transduced with CALRins5 and Untreated replicate 1


title: CALR INS clone C1

description: K562 cells transduced with LCALRins5IDN

value: clone 1


title: CALR DEL clone C1


title: CALR INS clone C51

description: K562 cells transduced with LCALRins5IDN


title: K562 CALR wild-type Melittin replicate 1

description: K562 transduced with CALR wild-type and treated with Melittin replicate 1


title: K562 CALRdel52 Melittin replicate 2

description: K562 transduced with CALRdel52 and treated with Melittin replicate 2


title: K562 CALRins5 Melittin replicate 1

description: K562 transduced with CALRins5 and treated with Melittin replicate 1


title: K562 CALRdel52 Untreated replicate 1

description: K562 transduced with CALRdel52 and Untreated replicate 1


title: M_1: MOCK treated rep1

status: Public on Aug 03 2019

city: Shenzhen

first: Tengbo

last: Huang

state: Guangdong

address: 1066 Xuanyuan Avenue

department: College of Life Sciences and Oceanography

institute: Shenzhen university

data_processing:
Library quality was evaluated using Quant-iTPicoGreen dsDNA Assay Kit (Life Technologies).
Sequencing was performed on Hiseq2500platform with sequencing kit TruSeq PE Cluster v3 (Illumina).
The raw reads were filtered and clean reads were aligned to the Arabidopsis reference genome (TAIR11) using STAR (Dobin and Gingeras, 2015)  with default settings.
DESeq2 (Love et al., 2014) was used to identify differentially expressed genes (P value < 0.05)
Genome_build: the Arabidopsis reference genome (TAIR11)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: MOCK treated_12-day old seedlings

growth_protocol: Arabidopsis thaliana plants were grown at 22±1°C under 14 hours illumination and 10 hours dark

extract_protocol:
Plants were frozen in liquid nitrogen for RNA extraction with Trizol (Life Technologies)
Libraries were prepared following the protocol of TruSeq RNA LT Sample Prep Kit v2 (Illumina)

treatment_protocol: 12 days old 35S:GR-TCP5 seedlings were treated with DEX (10 mM dexamethasone, 0.1% ethanol, 0.015% silwet-L77) or mock (0.1% ethanol, 0.015% silwet-L77) solutions for 4 hours

value: 35S:GR-TCP5 line

value: 12-day old seedlings

value: MOCK


title: M_3: MOCK treated rep3


title: D_3: DEX treated rep3

source_name: DEX treated_12-day old seedlings

value: DEX


title: M_2: MOCK treated rep2


title: D_2: DEX treated rep2


title: CALR WT clone C1

description: K562 cells transduced with LCALRwtIDN


title: D_1: DEX treated rep1


title: K562 CALRdel52 Melittin replicate 1

description: K562 transduced with CALRdel52 and treated with Melittin replicate 1

value: Melittin (MEL, 5ug/ml)

value: K562 Cell line, from human blood(chronic myelogenous leukemia)


title: siRNAs for Dmrt3/Dmrta2 set2_rep3

city: Kobe

first: Daijiro

last: Konno

address: 2-2-3 Minatojima Minamimachi Chuo-ku

department: Center for Developmental Biology (CDB)

country: Japan

institute: RIKEN

description: Gene expression at 24 hours after transfection with siRNA-set 2 for Dmrt3/Dmrta2

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent). On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome  Microarrays (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green, Green PMT is set to 100%, NoXDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Jan09 and Grid:026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Telencephalon, Dmrt3/Dmrta2 siRNAs-set 2, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using a combination of TRIZol reagent (Invitrogen) and QIAGEN RNeasy Mini RNA purification kit (QIAGEN) accortding to the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Indicated siRNAs and expression vectors for EGFPNLS were electroporated into the medial telencephalon of E11.5 CD1 mouse embryos. Transfected cells were isolated at 24 hours after electroporation by the cell sorter with GFP fluorescence.

tag: strain

value: telencephalon

tag: developmental stage


title: Dmrta2 overexpression_rep3

description: Gene expression at 24 hours after transfection with the expression plasmid for Dmrta2

source_name: Telencephalon, overexpression of Dmrta2, replicate 3


title: Dmrta2 overexpression_rep2

source_name: Telencephalon, overexpression of Dmrta2, replicate 2


title: Control siRNAs_rep2

description: Gene expression at 24 hours after transfection with control siRNAs

source_name: Telencephalon, control siRNAs, replicate 2


title: siRNAs for Dmrt3/Dmrta2 set1_rep2

description: Gene expression at 24 hours after transfection with siRNA-set 1 for Dmrt3/Dmrta2

source_name: Telencephalon, Dmrt3/Dmrta2 siRNAs-set 1, replicate 2


title: siRNAs for Dmrt3/Dmrta2 set1_rep3

source_name: Telencephalon, Dmrt3/Dmrta2 siRNAs-set 1, replicate 3


title: Dmrta2 overexpression_rep1

source_name: Telencephalon, overexpression of Dmrta2, replicate 1


title: siRNAs for Dmrt3/Dmrta2 set2_rep2

source_name: Telencephalon, Dmrt3/Dmrta2 siRNAs-set 2, replicate 2


title: Control siRNAs_rep3

source_name: Telencephalon, control siRNAs, replicate 3


title: siRNAs for Dmrt3/Dmrta2 set1_rep1

source_name: Telencephalon, Dmrt3/Dmrta2 siRNAs-set 1, replicate 1


title: siRNAs for Dmrt3/Dmrta2 set2_rep1

source_name: Telencephalon, Dmrt3/Dmrta2 siRNAs-set 2, replicate 1


title: Pull Bioitin OPC mirctr 3 [Dutta_miRNA_Pulldown_Set_2_RandID_5_S5]

city: Portland

first: Selva

last: Baltan

state: OR

address: 3181 S.W. Sam Jackson Park Rd.

department: Anesthesia and Perioperative Medicine (APOM)

institute: Oregon Health and Science University

data_processing:
Post-sequencing, raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 36.
Trimmed reads were then aligned using the HISAT2 aligner to the Mus musculus NCBI reference genome assembly (v GRCm38) and sorted using SAMtools.
Aligned reads were counted and assigned to gene meta-features using the program featureCounts part of the Subread package.
These count files were imported into the R programming language and were assessed for quality control, normalized, and analyzed using an in-house pipeline utilizing the edgeR Bioconductor library for differential gene expression testing.
Genome_build: mm8
Supplementary_files_format_and_content: Comma Separated Values (CSV) files include CPM values for each Sample ...

source_name: Pull Bioitin OPC mirctr

growth_protocol: OPCs proliferation in SATO+PDGFRA media

extract_protocol:
RNA isolated from biotin-tagged miRNA mimic (control and miR-27a)-transfected OPCs, as well as pulldown assays using TRIZOL method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: miRNA mimic transfection (Control and miR-27a)

tag: age

value: Post natal day 6-7

value: brain

value: Oligodendrocyte progenitor cells (OPCs)

value: biotin-tagged miRNA mimic control


title: Pull Bioitin OPC mir27a 1 [Dutta_miRNA_Pulldown_Set_2_RandID_2_S2]

source_name: Pull Bioitin OPC mir27a

value: biotin-tagged miRNA mimic miR-27a


title: Pull Bioitin OPC mir27a 3 [Dutta_miRNA_Pulldown_Set_2_RandID_6_S6]


title: Bioitin OPC mir27a 3 [Dutta_miRNA_Pulldown_Set_2_RandID_7_S7]

source_name: Bioitin OPC mir27a


title: Pull Bioitin OPC mirctr 1 [Dutta_miRNA_Pulldown_Set_2_RandID_11_S11]


title: Bioitin OPC mir27a 2 [Dutta_miRNA_Pulldown_Set_2_RandID_9_S9]


title: Bioitin OPC mir27a 1 [Dutta_miRNA_Pulldown_Set_2_RandID_8_S8]


title: mouse1_m_early adversity_1_rep1

source_name: medial prefrontal cortex

tag: technical replicate

tag: batch

value: medial prefrontal cortex

tag: gender

value: M

value: early adversity


title: Biotin OPC mir ctr 2 [Dutta_miRNA_Pulldown_Set_2_RandID_10_S10]

source_name: Biotin OPC mir ctr

tag: genotype/variation


title: Control siRNAs_rep1

source_name: Telencephalon, control siRNAs, replicate 1


title: Biotin OPC mir ctr 3 [Dutta_miRNA_Pulldown_Set_2_RandID_12_S12]


title: SOM4

city: New York

first: Juhee

last: Jeong

address: 345 E 24th St

department: Basic sciences and Craniofacial development

institute: New York University College of Dentistry

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format by using Illumina bcl2fastq software
Sequencing reads were aligned to the mouse genome mm10 using STAR aligner
Read counts were normalized and used to test for differential expression with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values' file with normalized counts for all genes in each sample, along with Fold Change and p value for the comparison of expression levels between EMM and SOM.

source_name: supraorbital cranial mesenchyme

extract_protocol:
Apical and basolateral areas of the head were dissected in ice cold PBS, and subject to dispase treatment 3 U/ml, 37 C, 10 min. Subsequently, the surface ectoderm and the brain were removed to isolate the mesenchyme, which was flash frozen on dry ice and stored at -80 C. After enough tissue was collected, it was homogenized with a pestle and QIAshredder (QIAgen), and total RNA was extracted using RNeasy Mini kit (QIAgen).
Illumina TruSeq kit following standard Illumina protocol

tag: genotype

value: wild type


title: SOM3


title: SOM2


title: Biotin OPC mir ctr 1 [Dutta_miRNA_Pulldown_Set_2_RandID_1_S1]

tag: cell type


title: Pull Bioitin OPC mir27a 2 [Dutta_miRNA_Pulldown_Set_2_RandID_3_S3]


title: SOM1


title: EMM4

source_name: early migrating cranial mesenchyme