title: 11K_M_131


title: 11K_M_1090

status: Public on Apr 22 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 11K_M_130


title: 11K_M_951


title: 11J_M_265


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title: 11K_M_302


title: Sample34_plusauto-plasmaplussara-25uM-3

city: New York

first: Dr. Chiara

last: Giannarelli

state: NY

address: 435 E 30th St

department: Cardiology

institute: NYU Langone Health

description: RNA bulk sequencing

library_source: transcriptomic

data_processing:
Quality control of RNA-seq data was performed using FastQC2 v.0.11.7, a final report was generated for each FASTQ file to
assess general sequencing quality.
Following that the raw reads were aligned
using STAR v.2.6.1d with hg38 as the reference genome. The gene-level expression counts were
computed with featureCounts function in the Subread package (v.1.6.3; parameters: -g gene_id)
using the human gene annotations from Gencode release 33.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: atherosclerotic plaque tissue

growth_protocol: Atherosclerotic surgical tissue was cut into homogenous small pieces (3 x 3 x 3 mm) and cultured in RPMI-1640 medium.

extract_protocol:
Total RNA from human atherosclerotic tissue was isolated using the gentleMACSTM Octo Dissociator (Miltenyi Biotec) homogenization protocol for total RNA isolation and the QIAzol Lysis Reagent (Qiagen, Cat.# 79306), followed by RNA clean-up using the RNAeasy Mini kit (Qiagen, Cat.# 74104). 2ng of RNA were used as input for library prep.
RNA libraries for RNA-seq were prepared using Low input Clontech SMART-Seq HT with Nxt HT poly-A library construction.

treatment_protocol:
Tissue was stimulated with RPMI-1640 plus autologous plasma at a final concentration of 20% with saracatinib (25 µM) or vehicle (DMSO) for 24 hours, 37C, 5%CO2.
Tissue was collected and stored in Allprotect Tissue Reagent (Qiagen) for RNA isolation and RNA sequencing analysis.

tag: tissue

value: atherosclerotic plaque tissue

tag: treatment

value: plasma stimulation + saracatinib


title: Sample34_plusauto-plasmaplussara-25uM-2

description: RNA bulk sequencing


title: Sample34_plusauto-plasma-2

description: RNA bulk sequencing

value: plasma stimulation + vehicle


title: Sample34_plusauto-plasma-3

description: RNA bulk sequencing


title: 11K_M_301


title: 11K_M_300


title: 11K_M_299


title: 11K_M_298


title: 11K_M_295


title: 11K_M_296


title: 11K_M_297


title: 11K_M_294


title: 11K_M_292


title: 11K_M_313


title: Sample34_plusauto-plasmaplussara-25uM-1

description: RNA bulk sequencing


title: 11K_M_291


title: Sample34_plusauto-plasma-1

description: RNA bulk sequencing


title: 11K_M_290


title: 11K_M_307


title: 4C_neurons_Meteor,Eomes

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
Data were analyzed using the UMI-4C package (Schwartzman et al., 2016).
Contacts within 10,000,000bp of the bait coordinates were summarized in bedGraph interaction files.
bedGraph files were converted to bigWig format using wigToBigWig.
Assembly: mm9
Supplementary files format and content: bigWig interaction files

source_name: neurons

growth_protocol: Neuronal differentiation was performed as previously described (Ying and Smith, 2003). Briefly, mESCs were grown for two passages in serum-based medium on MEF-free, gelatin-coated plates. Cells were then seeded on gelatin-coated plates (2x105 cells/6-well) in neuronal differentiation medium: 1:1 mixture of DMEM/F12 (Sigma) and Neurobasal medium (Gibco), supplemented with 0.5X B27 (Gibco), 0.5X N2 (Gibco), 1X Glutamax (Gibco), 0.1mM β-mercaptoethanol (Sigma), 25μg/ml BSA, and 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries). After four days, the cells were dissociated with 0.05% Trypsin (Biological Industries) and re-plated (3.5x105/6-well) on Poly-D-Lysine (Sigma) and Laminin (Life)-coated plates, in neuronal differentiation medium also containing 20ng/ml FGF2 (Peprotech). FGF2 was removed after 24hr and the cells were grown for an additional three days.

extract_protocol:
3C was carried out on 5x10^6 cells, essentially as described (Olivares-Chauvet et al., 2016), with the following slight modification: permeabilization buffer constitution was 10 mM Tris-HCl pH 8, 10 mM NaCl, 0.5% NP-40, supplemented with protease inhibitors.
4C libraries were prepared as described (Schwartzman et al., 2016). Bait coordinates in Table 1 of the publication.
4C

tag: cell line

tag: genotype/perturbation

value: WT

value: Meteor


title: pKO1_scRNAseq

library_source: transcriptomic single cell

data_processing:
Initial analysis was carried out as described in(Jaitin et al., 2014; Keren-Shaul et al., 2019).
Metacells were constructed and analyzed using the MetaCell package(Baran et al., 2019).
Assembly: mm9
Supplementary files format and content: RNA counts per cell

molecule: polyA RNA

source_name: mESCs

growth_protocol: mESCs were routinely grown on gelatin-coated plates on MEFs in serum-based medium: DMEM (Gibco) containing 15% ES-grade fetal calf serum (Biological Industries), 1X Sodium pyruvate (Gibco), 1X Nonessential amino acids (Gibco), 0.1mM β-mercaptoethanol (Sigma), 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries), and 10ng/ml LIF (Weizmann Proteomics Unit). Cells were passaged with 0.25% Trypsin (Biological Industries) every 2–3 days.

extract_protocol:
Cells were sorted into 384-well plates containing 2nM barcodes and lysis buffer.
MARS-seq barcoding and library preparation were carried out as previously described(Jaitin et al., 2014).

value: promoter KO


title: 11K_M_288


title: 11K_M_289


title: WT1_scRNAseq


title: 4C_mESCs_Eomes

value: Eomes


title: 4C_mESCs_Meteor


title: 11K_M_287


title: 11K_M_286


title: 4C_fKO2_Eomes

value: Meteor full-body KO


title: 4C_Ctrl_Eomes

growth_protocol: mESCs were routinely grown on gelatin-coated plates on MEFs in 2i medium: a 1:1 mixture of Neurobasal medium (Gibco) and Knockout DMEM (Gibco), supplemented with 1X B27 (Gibco), 1X N2 (Gibco), 1X Glutamax (Gibco), 1X Sodium pyruvate (Gibco), 1X Nonessential amino acids (Gibco), 0.1mM β-mercaptoethanol (Sigma), 52.5μg/ml BSA, 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries), 1μM PD 0325901 (Axon Medchem), 3μM CHIR 99021 (Axon Medchem), and 10ng/ml LIF (Weizmann Proteomics Unit). Cells were passaged with 0.25% Trypsin (Biological Industries) every 2–3 days.

value: empty vector


title: 4C_Rz_Eomes

value: Meteor ribozyme KD


title: 4C_WT5_Meteor

value: MeteorKO


title: 11K_M_284


title: 4C_WT5_Eomes


title: 4C_WT4_Meteor


title: 4C_WT4_Eomes


title: KD1_EBd4

data_processing:
Quantification using RSEM, run on a gtf were the last exon of each gene was extended by 2Kb to the 3’ direction if no other gene was found on the same strand within that distance, to ensure that reads falling outside the annotated genes were assigned correctly.
Assembly: mm9
Supplementary files format and content: RSEM quantification files

source_name: EBs day 4

growth_protocol: mESCs were depleted from MEFs by 20 min incubation on gelatin-coated plates, and seeded at 500cells/27µl drop in differentiation medium (serum-based mESC medium without Lif), on the lids of 10cm plates with PBS. On d2 drops were collected, combined, and transferred to non-adherent 10cm petri dishes in differentiation medium. On d4 EBs were collected.

extract_protocol:
Total RNA was extracted from cells using the Trizol reagent (TRI, Sigma-Aldrich) according to the manufacturer’s instructions.
Lexogen QuantSeq 3' mRNA-Seq

value: CRISPR/dCas9 KD of Meteor


title: 11K_M_293


title: Ctrl_EBd4


title: pInv_EBd4


title: pKO2_EBd4


title: pKO1_EBd4

value: Meteor promoter inversion


title: WT2_EBd4

value: Meteor promoter KO


title: WT1_EBd4


title: 11K_M_280


title: 11K_M_282


title: 11K_M_281


title: 11K_M_283


title: 11K_M_278


title: 11K_M_279


title: pKO2_H3K27me3_Rep3

data_processing:
Reads were aligned to the genome using bowtie2 v2.2.9 with default parameters except -X 2000
Signal tracks were generated using macs2 (v2.1.1) callpeak, with default parameters -f BAMPE --bdg --SPMR --broad -g mm
bedGraph files were converted to bigWig format using wigToBigWig
Assembly: mm9
Supplementary files format and content: bigWig read coverage files

extract_protocol:
Cut&Run was conducted essentially as described (Meers et al., 2019). Briefly, 2x105 cells were pelleted 3min at 600xg, washed twice in 1.5ml Wash buffer (20mM Hepes-Naoh pH 7.5, 150mM NaCl, 0.5mM Spermidine, and 1X protease inhibitors), and resuspended in 300µl Wash buffer. 10µl of BioMag Plus Concanavalin A beads (#BP531, WeisScientific) were washed twice in Binding buffer (20mM Hepes-KOH pH 7.9, 10mM KCl, 1mM CaCl2, and 40mM MnCl2), and added to the cells. Cell-bead mixture was rotated 5–10min at RT, magnetized, resuspended in 150μl Antibody buffer (Wash buffer with 0.15% Digitonin, 2mM EDTA, and 1.5μl of either H3K27me3 antibody (C36B11, Cell Signaling #9733) or H3K4me3 antibody (C42D8, Cell Signaling #9751), and incubated overnight at 4°C. Cells were washed twice in Dig-Wash buffer (Wash buffer also containing 0.15% Digitonin), resuspended in 150μl Dig-Wash buffer containing 350ng/ml pA-MNAse (Weizmann Proteomics Unit), and rotated 1h at 4°C. Cells were then washed twice with Dig-Wash buffer, resuspended in 100μl Dig-Wash buffer, and placed in ice water for a few minutes. MNAse was activated by adding 2μl of 100mM CaCl2 and incubating 30 min on ice. Reaction was stopped by adding 100μl 2X STOP buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.15% Digitonin, 100μg/ml RNAse A, and 50μg/ml glycogen). Chromatin fragments were released by incubating 30min at 37°C, transferring the sup to new tubes, and incubating 1h at 50°C with 1μl 20% SDS and 2.5μl 20mg/ml Proteinase K. DNA was isolated using phenol-chloroform extraction.
Library construction was done as described in (Janssens and Henikoff; Meers et al., 2019).

tag: antigen


title: 4C_fKO2_Meteor


title: 4C_KD1_Eomes


title: 11K_M_277


title: 11K_M_285


title: pKO1_H3K27me3_Rep3


title: WT1_H3K27me3_Rep3


title: WT2_H3K27me3_Rep3


title: 11K_M_276


title: 11K_M_275


title: Rz_Input

data_processing:
Reads were aligned to the genome using bowtie2 v2.2.9
Signal tracks were generated using macs2 (v2.1.1) callpeak, with default parameters except -f BAMPE --bdg --SPMR -g mm
Fold-enrichment was calculated using macs2 bdgcmp, with parameter -m FE
wigTobigWig
Assembly: mm9
Supplementary files format and content: bigWig read coverage files

extract_protocol:
Cells were fixed in 1% formaldehyde, 10min, RT; quenching with 125mM glycine.
ChIP was performed essentially as described (Rom et al., 2019), with the following slight modification: pellets were sonicated using a Bioruptor for either 12 (mESCs) or 15 (NPCs) cycles in high setting, 30sec ON, 30sec OFF. Antibodies used: H3K27ac (D5E4) (Cell Signaling #8173), and CTCF (D31H2) (Cell Signaling, #3418).


title: Rz_CTCF

value: CTCF


title: 11K_M_274


title: fKO2_CTCF


title: fKO2_Input


title: fKO1_Input


title: 11K_M_273


title: WT4_Input


title: WT4_CTCF


title: KD1_Input


title: 11K_M_272


title: KD1_CTCF


title: Ctrl_Input


title: Input_WT

source_name: NPCs

growth_protocol: Neuronal differentiation was performed as previously described (Ying and Smith, 2003). Briefly, mESCs were grown for two passages in serum-based medium on MEF-free, gelatin-coated plates. Cells were then seeded on gelatin-coated plates (2x105 cells/6-well) in neuronal differentiation medium: 1:1 mixture of DMEM/F12 (Sigma) and Neurobasal medium (Gibco), supplemented with 0.5X B27 (Gibco), 0.5X N2 (Gibco), 1X Glutamax (Gibco), 0.1mM β-mercaptoethanol (Sigma), 25μg/ml BSA, and 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries). NPCs were collected after four days.


title: tR2_4

city: Poznań

first: Aleksandra

last: Obrepalska-Steplowska

address: 20 Władysława Węgorka

country: Poland

institute: Institute of Plant Protection - National Research Institute

data_processing:
Adapters from samples subjected to differential gene expression analysis were trimmed with Skewer (version 0.2.2). The quality of the FASTQ files was analyzed with FastQC (version 0.11.5). Trimmed raw reads were aligned to the assembled transcriptome data obtained from the previous step using STAR (version 2.5.2b). Differential expression analysis between groups was performed with DESeq2 (version 1.24.0)  in R (version 3.6.1).
Assembly: Apera spica-venti transcripme assembly [pending]
Supplementary files format and content: tab-delimited text file including raw counts of sequencing reads.
Supplementary files format and content: DEGs.xlsx: Excel file includes a list of differentially expressed genes found in each comparison in the study.

organism: Apera spica-venti

source_name: leaves

growth_protocol: Apera spica-venti plants were grown in controlled conditions in the greenhouse (21°C).

extract_protocol:
Total RNA was extracted using 750 µl of TriReagent solution (Thermo Fisher Scientific, Waltham, MA, USA), precipitated with 2-propanol, and washed with 70% ethanol. The air-dried precipitate was suspended in nuclease-free water. Total RNA for sequencing was subjected to DNA digestion using RNase-free DNase I (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA concentration and purity (the 260 nm/230 nm and 260 nm/280 nm values) of each sample were estimated in NanoDrop ND‐2000 spectrophotometer (Thermo Fisher Scientific), while the RNA quality was assessed with 0.7% gel electrophoresis.
One hundred ng of total RNA was subjected to the preparation of the library using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, San Diego, CA, USA).

treatment_protocol: Plants at the 12-13 BBCH stage were treated with pinoxaden (Axial 50 EC, 50 g l-1 of a.i., Syngenta, (Basel, Switzerland). Plants were treated once with the following dose of the herbicide calculated as an active ingredient: 45 g ha−1.  Non-treated plants were taken as the controls. Eight hours after treatment with the herbicide, plant leaves were harvested, immediately frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

value: leaves

tag: genotype

value: resistant

value: treated


title: pInv_H3K27me3_Rep3

value: promoter inversion


title: fKO1_CTCF


title: Ctrl_CTCF


title: tR2_3


title: G6PCp  s33

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

data_processing:
The obtained cDNA fragment libraries were sequenced on an Illumina HiSeq2500
using default parameters (single read 1x50bp) in pools of multiple samples. The
fastQ files where aligned to build Mus_musculus.GRCm38 Ensemble Release 82
reference genome using HISAT with default settings.
Before gene quantification SAMtools was used to sort the aligned reads. The gene level quantification was  performed by HTSeq-count. The extracted raw count file (ENSG, counts) was analyzed in MADMAX. After transformation (log2CPM), normalization (Voom) was performed to generate the differentially expressed genes
Genome_build: Mus_musculus.GRCm38 Ensemble Release 82

extract_protocol:
For RNA sequencing, initial quality check and RNA quantification of the samples was performed by capillary electrophoresis using the LabChip GX (Perkin Elmer) non
degraded RNA-samples were used for subsequent sequencing analysis
Sequence libraries were generated using the 3’QuantSeq sample preparation kits (LeXogen).

treatment_protocol: Total RNA from liver was isolated using TRI-Reagent (Sigma-Aldrich Corp.)

value: Liver

tag: strain background

tag: Sex

value: Male

value: 13-18 weeks

tag: shRNA(aav)

value: shChrebp


title: 11K_M_268


title: G6PCp  s31


title: tR2_2


title: G6PCp  s30


title: tR1_3


title: 11K_M_266


title: 11K_M_265


title: tR1_2


title: G6PCp  s28


title: G6PCp  s27


title: tR1_1


title: 11K_M_264


title: tS2_4

value: susceptible


title: H3K27ac_WT

value: WT


title: 11K_M_270


title: G6PCp  s26


title: 11K_M_262


title: G6PCp  s25


title: tS2_2


title: tS2_3


title: 11K_M_267


title: G6PC  s24

value: shScramble


title: 11K_M_260


title: G6PC  s23


title: tS2_1


title: G6PCp  s29


title: 11K_M_259


title: tS1_4


title: G6PC  s22


title: 11K_M_258


title: 11K_M_263


title: 11K_M_257


title: 11K_M_261


title: 11K_M_256


title: tS1_3


title: G6PC  s21


title: tS1_1


title: G6PC  s19


title: tS1_2


title: 4C_NPCs_Meteor

value: Meteor


title: G6PC  s20


title: 4C_pInv_Eomes

value: Eomes


title: G6PC  s18


title: 4C_pKO2_Eomes


title: 4C_pKO1_Eomes


title: 4C_WT2_Eomes


title: 4C_WT1_Eomes


title: 11K_M_269


title: WTp  s14

source_name: WTp


title: G6PC  s17


title: WTp  s16


title: G6PCp  s32


title: WTp  s13


title: pInv_H3K27me3_Rep2


title: WTp  s11


title: WTp  s12


title: H3K4me3_NPCs


title: WTp  s10


title: WTp  s15


title: cR2_4

value: control


title: pKO2_H3K27me3_Rep2

value: promoter KO


title: cS2_4


title: cR2_3


title: cR1_4


title: cS2_3


title: cR2_2


title: cR2_1


title: cR1_1


title: WT2_H3K27me3_Rep2


title: pKO1_H3K27me3_Rep2


title: cR1_2


title: cR1_3


title: WT   s8

source_name: WT


title: WT   s7


title: WT   s6


title: WT1_H3K27me3_Rep2


title: cS2_1


title: pInv_H3K27me3_Rep1


title: cS2_2


title: cS1_4


title: pKO2_H3K27me3_Rep1


title: cS1_3


title: WT   s5


title: WTp   s9


title: pKO1_H3K27me3_Rep1


title: cS1_2


title: WT   s4


title: WT2_H3K27me3_Rep1


title: WT   s3


title: WT   s1


title: WT1_H3K27me3_Rep1


title: cS1_1


title: WT   s2


title: CTL, replicate 1, scRNAseq

city: Shanghai

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

country: China

institute: Shanghai OE Biotech Co., Ltd

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Freshly bone marrow cells were flushed from normal and irradiated mice. Then, red blood cells were removed using the Red Blood Cell Lysis Buffer. After incubated with anti-Lineage, anti-Sca1 and anti-c-Kit antibodies on ice for 30 min, cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Subsequently, LSKs were sorted using a FACSAriaIII sorter (BD Biosciences) according to above three surface markers. LSKs were washed in ice-cold PBS (Mg2+/Ca2+ free) and resuspended in PBS (Mg2+/Ca2+ free) supplemented with 0.04% v/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, LSKs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: LSKs

value: Bone marrow

value: 6-8 weeks old


title: MusFS3

status: Public on Apr 21 2023

city: Charlottesville

first: Yuanming

last: Liu

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

description: 10x Genomics

data_processing:
10X Cell Ranger pipeline (version 3.0.2) was used to demultiplex and align sequencing reads
Assembly: A custom “pre-mRNA” reference genome created from mouse reference genome RGCm38.98
Supplementary files format and content: H5 file; feature-barcode matrices

source_name: Superficial superior colliculus

extract_protocol:
Brains were harvested after rapid decapitation to avoid stress- or anesthesia-related changes in gene expression, cooled in ice-cold Hibernate-A for 2min, placed into a chilled stainless steel brain matrix and then sectioned coronally into 1mm thick slices containing the sSC (Bregma -3.0 mm to -5.0 mm). The sSC was then visualized under a dissecting microscope, micro-dissected approximately by knife cuts. Next, we homogenized the sSC in lysis buffer and separated nuclei from cellular debris using density gradient centrifugation. After resuspending the nuclei pellet, the concentration of nuclei was counted with propidium iodide by a CellDrop automated cell counter (DeNovix, Delaware, U.S.A.).
We used 10X Chromium Next GEM 3’ reagent kit v3.1 according to the manufacturer’s protocol (user guide revision D) to capture each nucleus’s poly-adenylated RNA in a droplet, process it into cDNA sequencing libraries, and sequenced them by Illumina Next-Seq 550 or Nova-Seq 6000 to an average of 35,998 mean reads per cell.
10X Chromium Next GEM 3’ reagent kit v3.1

value: Superficial superior colliculus

value: Female

value: Neural cells

value: Chat-GFP

value: 2-4 months


title: A. spica-venti - R (herbicide resistant)

data_processing:
According to Babineau M., Mahmood K., Mathiassen S.K., Kudsk P. & Kristensen M. (2017a) De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages. BMC Genomics 18, 1-12.
Assembly: Data subjected for de novo transcriptome assembly
Supplementary files format and content: APESV_transcriptome.FASTA - provides nucleotide sequences for the sequences for which blast results were obtained.
Supplementary files format and content: APESV_transcriptome_blastp.txt - the results of the protein BLAST

growth_protocol: Apera spica-venti plants were grown in controlled conditions in the greenhouse (16°C or 21°C).

treatment_protocol: Plants at the 12-13 BBCH stage were treated with the herbicides with the following active ingredients (a.i.): iodosulfuron-methyl sodium (Autumn WG 10, 100 g kg−1 of a.i., Bayer Crop Science, Leverkusen, Germany), pyroxulam (Nomad 75 WG, 75 g kg-1 of a.i., Corteva Agriscience, Wilmington, USA), pinoxaden (Axial 50 EC, 50 g l-1 of a.i., Syngenta, (Basel, Switzerland), and fenoxaprop-P-ethyl (Puma Uniwersal 069 EW, 69 g l-1 of a.i., Bayer Crop Science). Plants were treated once with the following doses of the herbicides calculated as an active ingredient: 10 g ha-1 for iodosulfuron-methyl sodium, 9 g ha−1 for pyroxsulam, 45 g ha−1 for pinoxaden, and 69 g ha−1 for fenoxaprop-P-ethyl.  Non-treated plants were taken as the controls. Three and seven days after treatment with the herbicide, plant leaves were harvested, immediately frozen in liquid nitrogen, and stored at -80°C until RNA extraction.

value: leaves

value: herbicide resistant


title: A. spica-venti - S (herbicide susceptible)

value: herbicide susceptible


title: MusFS2

description: 10x Genomics


title: IR, replicate 1, scRNAseq

description: 10x Genomics

value: irradiated (at day 15 after 5.0 Gy total body irradiation)


title: Human Brain Organoids, infected with sfRNA-deficeint ZIKV, 3dpi 2

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: MBS Bldg 76, Cooper Rd

department: School Of Chemistry And Molecular Biosciences

country: Australia

institute: The University of Queensland

data_processing:
TRIMMOMATIC v.0.36.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence (parameter- ILLUMINACLIP: TruSeq3-PE:2:30:10 LEADING:32 TRAILING:32 SLIDINGWIN-DOW:4:20 MINLEN:25)
Trimmed sequence reads were mapped to gh38 using HISAT2 v.2.1.0
Feature count was performed using HTSEQ v.0.9.1 in Union mode, with strand set to “Reverse”, end feature type set to “exon”
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes reads counts for all Samples

source_name: Brain Organoids

growth_protocol: Human embryonic stem cell line GENEA022 (Genea Biocells) was cultured on ECM Gel from Engelbreth-Holm-Swarm murine sarcoma (Sigma Aldrich, USA) in mTeSR medium (Stem Cell Technologies, USA). Brain organoids were generated using a protocol in which patterned embryoid bodies were expanded for 4 days in N2 medium (DMEM/F12 (Gibco, USA) with 1% N-2 supplement (Gibco, USA), 2% B-27 supplement (Gibco, USA), 1% MEM Non-Essential Amino Acids (Gibco, USA), 100 U/ml Penicillin and 100 ug/ml Streptomycin (Gibco, USA), 0.1% β-mercaptoethanol (Gibco, USA) with daily supple-mentation of 20 ng/mL bFGF (R&D, USA). Embryoid bodies were embedded in 15 ul of Matrigel (Stem Cell Technologies, USA) and media changed to 1:1 mixture of Neurobasal medium (Invitrogen, USA) and DMEM/F12 containing 1:200 MEM-NEAA, 1:100 Glu-tamax (Gibco, USA), 1:100 N2 supplement, 1:50 B27 supplement, 1s penicil-lin-streptomycin, 50 μM 2-mercaptoethanol and 0.25% insulin solution (Sigma, USA). Fresh media was replaced three times a week.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Ribo-Zero Gold Library Prep Kit following manufacturer's protocols.

treatment_protocol: Brain organoids were utilized for viral infection at day in vitro (DIV) 15. A virus inoculum containing of 105 FFU of each virus was added to a single organoid-containing well of 24-well plate and incubated at 37 °C O/N. Each ZIKV-infected organoid was then washed three times with culture media and transferred to a single well of a 24-well plate containing 500 μl of ND medium.

value: Brain Organoids

value: mixed, neural tissue

value: WT

value: Mutant ZIKV infection

tag: time

value: Day 3


title: Human Brain Organoids, infected with sfRNA-deficeint ZIKV, 3dpi 1


title: Human Brain Organoids, uninfected 2

value: Control


title: Human Brain Organoids, infected with WT ZIKV, 3dpi 2

value: WT ZIKV infection


title: TTseq_A375_cdk13_R860Q_rep1

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: TT-seq

data_processing:
We aligned RNA-seq and TT-seq data to hg38 and to the transcriptome (genecode v26 ‘basic’ annotations) with STAR (Dobin et al., 2013). For data with spike-ins, we also aligned to the spike-in genomes, but as we observed no statistically significant difference in percent spike-in reads we depth normalized both the RNA-seq and TT-seq data.
Read coverage bigWig files were generated by STAR and then normalized by read depth.
Assembly: hg38
Supplementary files format and content: Read depth-normalized read coverage bigWig files

source_name: A375 melanoma cell line

growth_protocol: Ribo-depleted RNA-seq and TT-seq were executed on equal numbers of human melanoma cells collected at the same time from pLENTI CMV CLOVER (n=3) and pLENTI CMV CDK13R860Q with spike in ERCC proportional to cell number (RNA-seq and TT-seq) (Thermofisher, 4456740) and 4sU labeled Drosophila S2 cell RNA (just TT-seq).

extract_protocol:
TT-seq 4sU pulse was 5min and is otherwise as published (Schwalb et al., 2016).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S) was used for library prep and samples were sequenced with paired end sequencing on a HiSeq 2500

treatment_protocol: RNA was collected in Trizol per standard protocol.

value: A375 melanoma cell line

value: pLENTI CMV CDK13 R860Q


title: TTseq_A375_Ctrl_rep2

description: TT-seq

value: pLENTI CMV CLOVER


title: TTseq_A375_Ctrl_rep3

description: TT-seq


title: TTseq_A375_Ctrl_rep1

description: TT-seq


title: TTseq_A375_cdk13_R860Q_rep3

description: TT-seq


title: RNAseq_A375_cdk13_R860Q_rep3


title: TTseq_A375_cdk13_R860Q_rep2

description: TT-seq


title: RNAseq_A375_cdk13_R860Q_rep2


title: RNAseq_A375_cdk13_R860Q_rep1


title: RNAseq_A375_Ctrl_rep3


title: RNAseq_A375_Ctrl_rep2


title: RNAseq_A375_Ctrl_rep1


title: MM057_BORIS_with_dox_Rep2

city: Montreal

first: Sanne

middle: Marlijn

last: Janssen

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

department: Pathology

country: Canada

institute: Lady Davis Institute for Medical Research

description:
BORIS_posDox_2.narrowPeak
BORIS_posDox_2_peaks.xls

data_processing:
Tiles which contained low-quality reads were removed, using the filterbytile.sh script from BBMap tool (Bushnell B. 2014; Bushnell et al. 2017), using default parameters. In addition, adapter contamination of the Nextera Transposase Sequence was removed using the trim_adapters script by atactk: a toolkit for ATAC-Seq data (Parker 2015); default parameters were used. Furthermore, the first 17 bp of all reads were trimmed with cutadapt (Martin 2011) to ensure high base quality.
trimmed reads were then aligned to the human reference genome (version GRCh38.p12) using BWA-MEM (Li 2013), with the following parameters: bwa mem -M -a -t 30 hg38.fa. read1.fastq read2.fastq.
duplicate alignments were marked and removed with Picard-Tools(Wysoker et al. 2009) MarkDuplicates tool, using the following command; picard.jar MarkDuplicates I=file_name.bam O=file_name.no_duplicates.bam M=file_name.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT.
After duplication removal, an additional filtering step was implemented with SAMtools, using the following command: samtools view -b -h -f 2 -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 20 -e chrM -e chrY -e ‘VN:’ file_name.bam. At the end of this sifting step, reads mapping to mitochondrial DNA (mtDNA) and Chromosome Y were excluded, in addition to reads that were not mapped/paired properly or mapped to multiple places in the genome. Lastly, reads with Q-score<20 were removed as well. Blacklisted regions as defined by the ENCODE file ENCFF419RSJ.bed, were removed
MACS2 call-peak function was used with the following command, customized for ATAC-Seq reads: macs2 callpeak -g hs -q 0.05 -f BAMPE -B.
Assembly: GRCh38.p12
Supplementary files format and content: narrowPeak files: bed files that contain the chromosomal locations of the called ATACseq peaks
Supplementary files format and content: excel files: output of MACS2 peak calling

source_name: skin

growth_protocol: MM057 cells were infected with the lentiviral vector pI20-EV or pI20-BORIS and selected by addition of 150μg/ml G418/Neomycin (Wisent, 450-130-QL). Upon selection, cell lines were maintained in the presence of 50μg/ml G418. For the RNA-seq experiments, cells were cultured in a treated 100mm tissue culture dish for five days either in the absence or presence of 50ng/ml doxycycline (Clontech, 631311). Doxycycline was refreshed every 48 hours. Cell culture medium: Ham’s F10 medium (Wisent, 318-050-CL) supplemented with 8% heat-inactivated fetal bovine serum (Wisent, 080- 450), 1% penicillin-streptomycin (Wisent, 450-201-EL), 1% GlutaPlus (Wisent, 609-066-EL) and 50μg/ml G418.

extract_protocol:
Cells were detached from the culture dish with citric saline (270mM KCl, 30mM sodium citrate), passed through a 40um filter and counted using a hemocytometer to collect 50.000 cells for all four experimental conditions. To isolate nuclei, cells were first lysed for 20 min on ice in lysis buffer 1 (0.1% Sodium citrate tribasic dehydrate (Sigma, S1804) and 0.1% Triton X-100 (Bioshop, TRX777.100)) followed by 20 min lysis on ice in lysis buffer 2 (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl, 0.1% Igepal CA630 (Bioshop, NON999.500) and 0.1% Tween-20 (Bioshop, TWN510.500). The nuclei were pelleted by centrifugation for 10min at 600g (4°C) and supernatant was carefully removed to reduce mitochondrial DNA (mtDNA) content. For the transposase reaction, the nuclei pellet was re-suspended in 25μl transposase reaction mix containing of 4μl Tn5 transposase in 1x transposase reaction buffer (Nextera DNA library kit, Illumina, FC-121–1030) and 0.1% Tween-20 (Bioshop, TWN510.500), and incubated for 30min at 37°C with gentle shaking (400rpm). Immediately following transposition, DNA was purified using the MinElute PCR purification Kit (Qiagen, 28004), according to manufacturer’s instructions.
Library fragments were amplified in two steps. First, 5 cycles of PCR were performed using NEBNext® High-Fidelity PCR master mix (New England BioLabs, M0541) with 1.25μM barcoded Nextera PCR primers (Supp 10.). in a final volume of 50μl on a BioRad C1000 Thermal Cycler. The cycling program used was as follows: 5 min at 72°C, 30 sec at 98°C, 5 times cycling for 10sec at 98°C, 30sec at 63°C and 1 min at 72°C. To reduce GC and size bias during library amplification, 5μl from the PCR mix was used for a 15μl qPCR side-reaction containing the same reagents with the addition of SYBRgreen (9X, Life Technologies, S7563) to determine the number of additional PCR cycles and stop amplification prior to saturation. The CFX96 TouchTM (Bio-Rad, 1855196) qPCR machine was used with the following cycling conditions: 30 sec at 98°C, 20 times cycling for 10sec at 98°C, 30sec at 63°C and 1 min at 72°C followed by melt curve analysis. Using the CFX ManagerTM Software (Bio-Rad), the fluorescent intensity was plotted versus cycle number and the additional number of cycles was established as the cycle number corresponding to 1/4th of the maximum fluorescent intensity. Next, the initial PCR reaction mix was amplified for 3 additional PCR cycles. Library preparation for each experimental condition was performed in triplicate and samples were combined post PCR amplification for quality controls and sequencing. the library was size selected using KAPA Pure Beads (0.55X-1.8X; Roche, 7983298001) to enrich for 150-750 bp fragments. DNA of the libraries was submitted to the McGill University and Genome Québec Innovation Centre and fragment distribution was assessed by TapeStation (Agilent), libraries were quantified using Quant-iTTM PicoGreen® dsDNA Reagent® (ThermoFisher Scientific), pooled and sequenced paired-end (100bp read length) on one lane of an Illumina HiSeq4000.

value: skin

value: melanoma

value: cultured in the presence of 50ng/ml doxycycline for 5 days


title: Human Brain Organoids, uninfected 1


title: Human Brain Organoids, infected with WT ZIKV, 3dpi 1


title: H. pylori Su2_wt_replicate2

city: Muenchen

first: Christine

last: Josenhans

address: Pettenkoferstrasse 9a

department: Max von Pettenkofer Institute

country: Germany

institute: LMU Munich

data_processing:
CLC genomics workbench v 20.0 (Qiagen)
Sequence reads were downsampled to 2 Mio reads
Trimmed and quality-filtered downsampled reads were mapped to AE000511_HP reference genome.
RNA-Seq function of CLC genomics workbench was used to calculate transcript parameters for each gene
Assembly: AE000511_HP reference genome
Supplementary files format and content: excel files (xlsx) include RNA-seq parameters for each sample

organism: Helicobacter pylori

source_name: strain Su2

growth_protocol: For transcriptome analyses, H. pylori was harvested after 20 h growth from blood agar plates. Bacterial pellets were snap frozen in liquid nitrogen and stored at -80°C, until further processing for RNA purification and analysis.

extract_protocol:
RNA was harvested using bead homogenisation and RNEasy mini kit (Qiagen). Approximately 0.5 ug of total RNA of each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TrueSeq mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: strain Su2

value: bacteria

value: wild type (wt)


title: H. pylori Su2_∆cagPAI_replicate1

value: {delta}cagPAI


title: H. pylori Su2_∆cagPAI_replicate2


title: MM057_EV_with_dox_Rep2

description:
EV_posDox_2.narrowPeak
EV_posDox_2_peaks.xls


title: H. pylori Su2_wt_replicate1


title: MM057_BORIS_no_dox_Rep2

description:
BORIS_negDox_2.narrowPeak
BORIS_negDox_2_peaks.xls

value: cultured in the absence of doxycyclin for 5 days


title: MM057_BORIS_with_dox_Rep1

description:
BORIS_posDox_1.narrowPeak
BORIS_posDox_1_peaks.xls


title: MM057_EV_no_dox_Rep1

description:
EV_negDox_1.narrowPeak
EV_negDox_1_peaks.xls


title: MM057_EV_no_dox_Rep2

description:
EV_negDox_2.narrowPeak
EV_negDox_2_peaks.xls


title: MM057_EV_with_dox_Rep1

description:
EV_posDox_1.narrowPeak
EV_posDox_1_peaks.xls


title: P40_pIC_M1

city: Freiburg im Breisgau

first: Omar

last: Mossad

address: Breisacher str 64

department: Institute of Neuropathology

institute: University Hospital Freiburg

data_processing:
CASAVA1.8.2 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using STAR
read counts were extracted using featurecounts
differential gene expression analysis was performed using Deseq2 v.2.11.40.6
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: microglia

extract_protocol:
Mice were anesthetized and transcardially perfused with ice cold PBS. Brain hemispheres were homogenized and subjected to 37% / 70% percoll density gradient separation. Microglia cells were collected from the pellet of 37% percoll and washed extensively with FACS buffer (0.5% FBS in PBS) followed by staining with anti-CD11b (clone M1/70, eBioscience) and anti-CD45 (clone 30-F11, eBioscience) antibodies. Isolation of immune cells and flow cytometry.
Total RNA was extracted from FACS sorted CD11b+CD45lowLin- microglia cells using The ARCTURUS® PicoPure® RNA Isolation Kit (ThermoFisher) according to manufacturer’s protocol. The SMARTer v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 to 750 pg total-RNA. Double stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). One-hundered and fifty pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposase. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 or HiSeq 2000 System User Guide. Image analysis and base calling resulted in BCL files, which were converted into FATSQ files with the CASAVA1.8.2 software. Library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany).

value: Whole brain

value: Male


title: P40_pIC_M4


title: P40_ctr_M1

value: control


title: P40_pIC_F2

value: Female


title: P40_ctr_M3


title: P40_ctr_M4


title: P40_pIC_F3


title: P40_pIC_F4


title: P40_ctr_F3


title: P40_ctr_F2


title: MM057_BORIS_no_dox_Rep1

description:
BORIS_negDox_1.narrowPeak
BORIS_negDox_1_peaks.xls


title: P7_pIC_M4


title: 11K_M_271

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


title: siMLX_Donor_C_28

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: Novo Nordisk Research Centre Oxford

data_processing:
Adaptor trimming with Trim Galore! (v. 0.6.4_dev)
Alignement with Salmon (v. 1.9.0) (with --noLengthCorrection and --numBootstraps 100 argument)
Gene levels counts and counts obtained with Sleuth v. 0.30.0)
Assembly: GRCh38, release 38
Supplementary files format and content: gene_level_scaled_reads_per_base_matrix.txt (raw counts), gene_level_tpm_matrix.txt (tpm counts)

source_name: Primary Human Hepatocytes

growth_protocol: Primary human hepatocytes maintained in modified 5C PHH maintenance medium

extract_protocol:
Dynabeads mRNA DIRECT Kit
QuantSeq 3’mRNA-Seq Library Prep Kit-FWD

treatment_protocol: PHH were transfected with siRNA 7 days post seeding and RNA extracted 10 days post transfection

value: Primary Human Hepatocytes

tag: sirna

value: siMLX

tag: donor


title: siMLX_Donor_C_29


title: P7_pIC_M3


title: siMLX_Donor_C_27


title: Gbi_48h

city: Hangzhou

first: Yue

last: SUN

state: Zhejiang

address: Yuhangtang Rd

institute: Zhejiang University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: Gossypium bickii (G1) genome JZU_v1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Gossypium bickii

source_name: cotyledons

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: cotyledons

tag: developmental stage

value: 48-hours after imbibition


title: P7_pIC_M2


title: siMLX_Donor_B_24


title: siMLX_Donor_C_25


title: siMLX_Donor_C_26


title: siMLX_Donor_B_23


title: P7_pIC_M1


title: P7_ctr_M4


title: P7_ctr_M3


title: P7_ctr_M1


title: P7_ctr_M2


title: siMLX_Donor_B_21


title: P40_ctr_F1


title: siMLX_Donor_A_19


title: siMLX_Donor_A_20


title: siMLX_Donor_A_18


title: P7_pIC_F1


title: P7_pIC_F3


title: P7_pIC_F4


title: tR2_1

value: leaves

value: resistant

value: treated


title: tR1_4


title: siNT_Donor_C_15

value: siNT


title: siMLX_Donor_A_16


title: P7_ctr_F3


title: P7_ctr_F4


title: P7_ctr_F2


title: eds1-12 leaf, Pst DC3000 avrRps4 and NAM, replicate 3 sample 2

city: Carrboro

first: Dor

last: Russ

state: NORTH CAROLINA

address: 222 Old Fayetteville Rd, Apt. L103

department: Biology

institute: UNC Chapel Hill

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to TAIR10 genome using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: TAIR10
Supplementary files format and content: xlsx file containing log2 fold change values (compared to mock treated col-0), FDR adjusted p-values and gene expression data (RPKM) for each gene

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Qiagen rnaeasy 96.
Kappa hyper prep from 500ng of mRNA

value: leaf

tag: infection

value: Pst DC3000 avrRps4

value: NAM


title: eds1-12 leaf, Pst DC3000 avrRps4 and NAM, replicate 2 sample 2


title: siNT_Donor_C_14


title: siNT_Donor_C_13


title: siNT_Donor_C_12


title: siMLX_Donor_B_22


title: eds1-12 leaf, Pst DC3000 avrRps4 and NAM, replicate 1 sample 2


title: siNT_Donor_B_10


title: siNT_Donor_C_11


title: eds1-12 leaf, Pst DC3000 avrRps4 and NAM, replicate 3 sample 1


title: eds1-12 leaf, Pst DC3000 avrRps4 and NAM, replicate 1 sample 1


title: siNT_Donor_B_9


title: eds1-12 leaf, Pst DC3000 avrRps4, replicate 2 sample 2


title: eds1-12 leaf, Pst DC3000 avrRps4, replicate 3 sample 2


title: eds1-12 leaf, Pst DC3000 avrRps4, replicate 1 sample 2


title: siNT_Donor_B_8


title: siNT_Donor_B_7


title: siNT_Donor_A_5


title: siNT_Donor_B_6


title: siNT_Donor_A_4


title: eds1-12 leaf, Pst DC3000 avrRps4, replicate 3 sample 1


title: siMLX_Donor_A_17


title: P7_pIC_F2

tag: age


title: siNT_Donor_A_3


title: eds1-12 leaf, Pst DC3000 avrRps4, replicate 1 sample 1


title: P7_ctr_F1

tag: strain


title: eds1-12 leaf, Pst DC3000 avrRps4, replicate 2 sample 1

tag: tissue


title: siNT_Donor_A_2


title: eds1-12 leaf, Pst DC3000 EV and NAM, replicate 3 sample 2

value: Pst DC3000 EV

tag: treatment


title: siNT_Donor_A_1


title: eds1-12 leaf, Pst DC3000 EV and NAM, replicate 2 sample 2


title: RRBS_Jurkat-SV_5-aza-dC_rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

data_processing:
Raw reads were mapped to the in silico bisulfite converted human reference genome (GRCh37; hg19) by using Bismark v.0.23.0 with and non directional parameter applied. Only the uniquely mapped reads were used to make cytosine methylation calls by using bismark methylation extractor
Differentially methylated CpGs (dmCpGs) were identified by using the R package methylKit (v1.20.0)
Assembly: hg19
Supplementary files format and content: bedGraph files

source_name: Human SV-engineered Jurkat cells

growth_protocol: Human leukemia cell lines were cultured in RPMI supplemented with 20% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For RRBS, 1 x 106 cells were lysed, incubated with RNAse A and Proteinase K, and genomic DNA was purified using Monarch Genomic DNA purification kit (New England Biolabs). 0.5 - 1 ug of genomic DNA was digested with MspI for 2 hours and digested DNA was extracted using phenol/chloroform and purified by ethanol precipitation. MspI-digested DNA was incubated with Klenow Fragment, exo- (New England Biolabs) and dNTPs (10 mM dATP, 1 mM dGTP, 1 mM dCTP) for 30 min at 30°C  followed by 30 min at 37°C to perform end-repair and A-tailing, respectively. Methylated Illumina adapter (New England Biolabs) was ligated to end-repaired, A-tailed using T4 DNA ligase followed by digestion with USER enzyme mix (New England Biolabs). Size selection of 40-220bp inserts was performed by gel extraction from 3% NuSieve 3:1 (Lonza) agarose gel. Extracted DNA libraries underwent two consecutive rounds of bisulfite conversion using EpiTect Bisulfite kit (QIAGEN). Final RRBS libraries were constructed by PCR using NEBNext Index Primers for Illumina (New England Biolabs) and PfuTurbo Cx Hotstart polymerase (Agilent Technologies).

treatment_protocol: For 5-aza-dC treatments, 5 µM of 5-aza-dC was added to culture medium for 3 days. Every 24 hours, cells were collected by centrifugation and spent media was replaced with fresh cell culture medium and 5 µM of 5-aza-dC. DMSO diluted 1:10,000 was added to cell culture medium freshly in the same manner as for 5-aza-dC-treated cells to serve as negative control.

tag: cell line

value: Human SV-engineered Jurkat cells

tag: agent


title: eds1-12 leaf, Pst DC3000 EV and NAM, replicate 1 sample 2


title: eds1-12 leaf, Pst DC3000 avrRps4 and NAM, replicate 2 sample 1


title: RRBS_Jurkat-SV_5-aza-dC_rep1


title: eds1-12 leaf, Pst DC3000 EV and NAM, replicate 3 sample 1


title: eds1-12 leaf, Pst DC3000 EV and NAM, replicate 2 sample 1


title: RRBS_Jurkat-SV_DMSO_rep2

value: DMSO


title: RRBS_Jurkat-SV_DMSO_rep1


title: eds1-12 leaf, Pst DC3000 EV and NAM, replicate 1 sample 1


title: eds1-12 leaf, Pst DC3000 EV, replicate 3 sample 2


title: RRBS_Jurkat-WT_5-aza-dC_rep2

source_name: Human wild-type Jurkat cells

value: Human wild-type Jurkat cells


title: eds1-12 leaf, Pst DC3000 EV, replicate 2 sample 2


title: eds1-12 leaf, Pst DC3000 EV, replicate 1 sample 2


title: eds1-12 leaf, Pst DC3000 EV, replicate 3 sample 1


title: eds1-12 leaf, Pst DC3000 EV, replicate 2 sample 1


title: RRBS_Jurkat


title: eds1-12 leaf, Pst DC3000 EV, replicate 1 sample 1


title: Col-0 leaf, Pst DC3000 avrRps4 and NAM, replicate 3 sample 2


title: RRBS_UT308

source_name: Leukemia patients

value: leukemia cells


title: Col-0 leaf, Pst DC3000 avrRps4 and NAM, replicate 1 sample 2


title: Col-0 leaf, Pst DC3000 avrRps4 and NAM, replicate 2 sample 2


title: RNA-seq_Jurkat_TLX3-OE_rep3

data_processing:
Sequencing reads from all RNA-seq experiments were aligned to human (hg19) reference genome by STAR 2.5.2b with the parameters: --outFilterMultimapNmax 1
The number of reads aligned to GENCODE annotated genes' exons were normalized to be of unit TPM (transcripts per million).
Assembly: hg19
Supplementary files format and content: text file of gene TPM values

source_name: Leukemia cell line

growth_protocol: Human MKPL-1, KBM-7, THP-1, U-937, MOLM-13, and HNT-34 leukemia cell lines were cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin. Human GDM-1, DND-41, Jurkat, and LOUCY leukemia cell lines were cultured with RPMI medium containing 20% FBS and 2% penicillin/streptomycin. Human MV-4-11 and K562 leukemia cell lines were cultured with IMDM supplemented with 10% FBS and 1% penicillin/streptomycin. Human HL-60 leukemia cell line was cultured with IMDM containing 20% FBS and 1% penicillin/streptomycin

extract_protocol: 0.1-1 ug of human leukemia patient RNA was processed for library generation using Ovation Ultralow RNA-seq system v2 (NuGEN). 0.1-1 ug of total human leukemia cell line RNA was processed for library generation using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra II Directional RNA Library Prep Kit.

value: Jurkat


title: RNA-seq_Jurkat_TLX3-OE_rep1


title: Col-0 leaf, Pst DC3000 avrRps4 and NAM, replicate 2 sample 1


title: RNA-seq_Jurkat_control_rep3

value: control


title: RNA-seq_Jurkat_control_rep2


title: Col-0 leaf, Pst DC3000 avrRps4 and NAM, replicate 1 sample 1


title: Col-0 leaf, Pst DC3000 avrRps4, replicate 3 sample 2


title: Col-0 leaf, Pst DC3000 avrRps4, replicate 2 sample 2


title: RNA-seq_DND-41_shTLX3_rep2


title: RNA-seq_Jurkat_control_rep1


title: Col-0 leaf, Pst DC3000 avrRps4, replicate 1 sample 2


title: RRBS_Jurkat-WT_5-aza-dC_rep1


title: RNA-seq_DND-41_shTLX3_rep1


title: Col-0 leaf, Pst DC3000 avrRps4, replicate 3 sample 1


title: RNA-seq_DND-41_shRen_rep2

value: shRen


title: Col-0 leaf, Pst DC3000 avrRps4, replicate 2 sample 1


title: RRBS_Jurkat-WT_DMSO_rep1


title: RRBS_Jurkat-WT_DMSO_rep2


title: RNA-seq_DND-41_shRen_rep1


title: Col-0 leaf, Pst DC3000 avrRps4, replicate 1 sample 1


title: RRBS_DND-41

source_name: Human DND-41 cells

value: Human DND-41 cells


title: RNA-seq_Jurkat-SV_5-aza-dC_rep3

value: Jurkat-SV


title: Col-0 leaf, NAM treated, replicate 3 sample 2


title: Col-0 leaf, NAM treated, replicate 2 sample 2


title: RRBS_UT242


title: RNA-seq_Jurkat-SV_5-aza-dC_rep2


title: RNA-seq_Jurkat-SV_5-aza-dC_rep1


title: RNA-seq_Jurkat_TLX3-OE_rep2


title: Col-0 leaf, NAM treated, replicate 1 sample 2


title: Col-0 leaf, Pst DC3000 avrRps4 and NAM, replicate 3 sample 1


title: RNA-seq_Jurkat-SV_DMSO_rep3


title: RNA-seq_Jurkat-SV_DMSO_rep2


title: Col-0 leaf, NAM treated, replicate 2 sample 1


title: RNA-seq_Jurkat-SV_DMSO_rep1


title: Col-0 leaf, NAM treated, replicate 1 sample 1


title: RNA-seq_Jurkat-WT_5-aza-dC_rep3

value: Jurkat-WT


title: RNA-seq_Jurkat-WT_5-aza-dC_rep2


title: Col-0 leaf, mock treated, replicate 2 sample 2

value: mock


title: Col-0 leaf, mock treated, replicate 1 sample 2


title: Col-0 leaf, mock treated, replicate 3 sample 1


title: RNA-seq_Jurkat-WT_DMSO_rep3


title: RNA-seq_Jurkat-WT_DMSO_rep2


title: RNA-seq_Jurkat-WT_DMSO_rep1


title: Col-0 leaf, mock treated, replicate 1 sample 1


title: Col-0 leaf, Pst DC3000 EV and NAM, replicate 3 sample 2


title: Col-0 leaf, Pst DC3000 EV and NAM, replicate 2 sample 2


title: RNA-seq_THP-1


title: RNA-seq_U-937


title: RNA-seq_MV-4-11


title: Col-0 leaf, Pst DC3000 EV and NAM, replicate 3 sample 1


title: RNA-seq_MOLM-13


title: RNA-seq_MKPL-1


title: Col-0 leaf, Pst DC3000 EV and NAM, replicate 2 sample 1


title: RNA-seq_KBM-7


title: RNA-seq_K-562


title: Col-0 leaf, Pst DC3000 EV and NAM, replicate 1 sample 1


title: Col-0 leaf, NAM treated, replicate 3 sample 1


title: Col-0 leaf, Pst DC3000 EV, replicate 3 sample 2


title: RNA-seq_Jurkat


title: Col-0 leaf, Pst DC3000 EV, replicate 2 sample 2


title: RNA-seq_HNT-34


title: Col-0 leaf, Pst DC3000 EV, replicate 1 sample 2


title: RNA-seq_HL-60


title: Col-0 leaf, Pst DC3000 EV, replicate 3 sample 1


title: RNA-seq_GDM-1


title: RNA-seq_Jurkat-WT_5-aza-dC_rep1


title: Col-0 leaf, mock treated, replicate 3 sample 2


title: Col-0 leaf, Pst DC3000 EV, replicate 2 sample 1


title: RNA-seq_DND-41


title: Col-0 leaf, mock treated, replicate 2 sample 1


title: Col-0 leaf, Pst DC3000 EV, replicate 1 sample 1


title: ADR1-L2 D484V 26.6 leaf, replicate 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to TAIR10 genome using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: TAIR10
Supplementary files format and content: xlsx file containing log2 fold change values (compared to col-0), FDR adjusted p-values and gene expression data (RPKM) for each gene


title: ADR1-L2 D484V leaf, replicate 3

value: ADR1-L2 D484V


title: RNA-seq_UT448

source_name: Leukemia patient

value: Blood


title: RNA-seq_UT445


title: ADR1-L2 D484V 30.4 leaf, replicate 3

value: leaf


title: RNA-seq_UT434

value: Bone Marrow


title: RNA-seq_UT452


title: RNA-seq_UT422


title: ADR1-L2 D484V 30.4 leaf, replicate 2


title: Col-0 leaf, Pst DC3000 EV and NAM, replicate 1 sample 2

value: NAM


title: RNA-seq_UT424


title: ADR1-L2 D484V 26.6 leaf, replicate 2


title: RNA-seq_UT413


title: ADR1-L2 D484V leaf, replicate 2


title: RNA-seq_UT397


title: Col-0 leaf, replicate 3


title: ADR1-L2 D484V 26.6 leaf, replicate 1


title: RNA-seq_UT390


title: RNA-seq_UT382


title: ADR1-L2 D484V leaf, replicate 1


title: RNA-seq_UT380


title: Col-0 leaf, replicate 1


title: RNA-seq_UT375


title: RNA-seq_UT370


title: RNA-seq_UT308


title: RNA-seq_UT292


title: RNA-seq_UT289


title: RNA-seq_UT287


title: RNA-seq_UT278


title: RNA-seq_UT273


title: RNA-seq_UT270


title: Col-0 leaf, replicate 2


title: RNA-seq_UT393


title: ADR1-L2 D484V 30.4 leaf, replicate 1


title: male_F3_control_rep4 (xcm)

type: RNA

city: New Delhi

first: Abhay

last: Sharma

state: Delhi

address: Sukhdev Vihar, Mathura Road

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

description: Gene expression data from w1118 flies free of all transgenic constructs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at  45 °C on GeneChip Drosophila Genome 2.0 Array. The hybridized arrays were washed and stained in Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix® GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed using the Bioconductor suite for R and the limma package (version 3.46.0). Probe intensities were corrected for background hybridization using GC-RMA and quantile normalized within each sex.

label: biotin

organism: Drosophila melanogaster

source_name: F3 descendant of the control lineage

label_protocol: Biotinylated cRNA were prepared using the GeneChip® 3’ IVT PLUS Reagent Kit starting with 100 ng total RNA.

growth_protocol: The flies were kept at 25 °C on a 12-hour night-day cycle. To obtain each sample, 150 males and females were mated on BDSC semi-defined medium and their progeny eclosing within the first five days were collected.

extract_protocol: RNA was extracted by homogenizing 80-90 flies suspended in Trizol with zirconia beads.

treatment_protocol: The test lineage was established by breeding in the transgenic constructs from the ilp3-GAL4 line (obtained from Michael Pankratz) and the UAS-rpr line (BDSC #5824), and the CyO-YFP and Ser-GFP balancers into the w1118 background. Descendants of the test lineage were derived by crossing its males with females from the w1118 control lineage.

tag: batch

value: male

tag: generation

tag: lineage

tag: replicate


title: RNA-seq_UT263


title: female_F1_test_rep2 (n9.1)

description: Gene expression data from flies missing one of the constructs required to ablate insulin-producing cells

source_name: F1 descendant of the test lineage

tag: Sex

value: female

value: test

tag: genotype

value: cyo/+; dilp3/+


title: male_F1_test_rep2 (n6)


title: RNA-seq_UT320


title: male_F0_test_rep2 (n2)

description: Gene expression data from flies carrying both the constructs required to ablate insulin-producing cells with balancers

source_name: F0 founder of the test lineage raised concurrently with the F1 test and F1 control

value: rpr/cyo; dilp3/ser


title: RNA-seq_UT258


title: RNA-seq_UT254


title: male_F1_test_rep2 (n7)

description: Gene expression data from flies carrying both the constructs required to ablate insulin-producing cells without balancers

value: rpr/+; dilp3/+


title: RNA-seq_UT343


title: female_F1_control_rep2 (n18)

source_name: F1 descendant of the control lineage; serves as control for both F0 test and F1 test

value: control


title: RNA-seq_UT249


title: male_F1_test_rep2 (n5)

description: Gene expression data from flies carrying only balancer chromosomes

value: cyo/+; ser/+


title: RNA-seq_UT248


title: female_F0_test_rep2 (n4)


title: male_F3_test_rep4 (xtm)

source_name: F3 descendant of the test lineage


title: RNA-seq_UT242


title: male_F1_control_rep2 (n16)


title: female_F1_control_rep1 (f7b)


title: male_F1_test_rep2 (n8)

value: rpr/+; ser/+


title: RNA-seq_UT218


title: RNA-seq_UT216


title: male_F1_test_rep1 (f9)


title: female_F1_test_rep2 (n10.2)


title: RNA-seq_UT196


title: RNA-seq_UT261


title: female_F0_test_rep1 (f6)


title: female_F1_test_rep1 (f5)


title: RNA-seq_UT194


title: RNA-seq_UT175


title: RNA-seq_UT168


title: RNA-seq_UT096


title: female_F1_test_rep1 (f2b)


title: HiC_UT242

data_processing:
Raw reads were trimmed using cutadpat (version 1.8.3) with -m 10 -q 20. Trimmed reads were then processed using HiC-Pro (version 2.11.3). HiC-Pro covers the whole analysis from fastq files to the interaction matrix.
Assembly: hg19
Supplementary files format and content: iced and binned matrix (10kb). The format of the matrix is the standard cool matrix format.

source_name: Leukemia cells

extract_protocol: Hi-C libraries were prepared based on the in situ Hi-C protocol 16 with minor modifications. Briefly, 5 x 106 cells were cross-linked with 1% formaldehyde (Sigma #252549) for 10 min with gentle rotation and quenched with 125 mM glycine. Cells were washed twice with ice-cold PBS and cells were snap-frozen on dry ice for 30 min. Cell pellets were resuspended in 1 mL ice-cold cell lysis buffer and rotated for 30 min at 4°C.

value: Leukemia cells


title: 4C-seq_Jurkat-SV_5-aza-dC_TLX3-promoter_rep3

description: DpnII-Csp6I digested genomic DNA

data_processing:
Library strategy: 4C-seq
Sequencing reads were processed using pipe4C (https://github.com/deLaatLab/pipe4C). Raw reads were trimmed to keep the sequences after DpnII restriction site 'GATC' and including only reads that contain the Csp6I restriction site 'GTAC' ("nonblind" fragments). Trimmed reads were aligned to human hg19 genome assembly using Bowtie2. The top 2 fragments were excluded from normalization and the normalization factor was set to 1000000. Following normalization, the data was smoothed by averaging using a running mean with a window size set to 100-bp.
The bigwig files were generated by converting the output wig files using the wigToBigWig function.
Assembly: hg19
Supplementary files format and content: bigwig files

extract_protocol: For 4C-seq analysis using the Illumina NextSeq500, 5 x 106 cells were cross-linked with 2% formaldehyde and nuclei were collected after cell lysis. Fixed chromatin was digested in situ with DpnII followed by in situ proximity ligation using T4 DNA ligase. Chromatin was then reverse cross-linked and genomic DNA was purified using phenol/chloroform extraction followed by ethanol precipitation. Purified DNA was then digested with Csp6I followed by proximity ligation with T4 DNA ligase. 4C templates were purified using QIAquick Spin columns. First round of PCR was performed using reading and non-reading promoter viewpoint primers followed by second round of PCR with primers containing Illumina-compatible adapter sequences.

treatment_protocol: For 5-aza-dC treatments, 5 µM of 5-aza-dC was added to culture medium for 7 days. Every 24 hours, cells were collected by centrifugation and spent media was replaced with fresh cell culture medium and 5 µM of 5-aza-dC. DMSO diluted 1:10,000 was added to cell culture medium freshly in the same manner as for 5-aza-dC-treated cells to serve as negative control.

value: Human SV-engineered Jurkat cells


title: 4C-seq_Jurkat-SV_5-aza-dC_TLX3-promoter_rep2

description: DpnII-Csp6I digested genomic DNA


title: female_F1_test_rep1 (f3)


title: female_F1_test_rep2 (n11.2)


title: male_F0_test_rep1 (f13)


title: male_F1_test_rep1 (f12.2)


title: RNA-seq_UT171


title: 4C-seq_Jurkat-SV_DMSO_TLX3-promoter_rep2

description: DpnII-Csp6I digested genomic DNA


title: 4C-seq_Jurkat-SV_DMSO_TLX3-promoter_rep3

description: DpnII-Csp6I digested genomic DNA


title: 4C-seq_Jurkat-SV_TLX3-promoter

description: DpnII-Csp6I digested genomic DNA


title: 4C-seq_Jurkat-SV_5-aza-dC_TLX3-promoter_rep1

description: DpnII-Csp6I digested genomic DNA


title: male_F1_test_rep1 (f10.3)


title: 4C-seq_Jurkat-WT_BCL11B-promoter

description: DpnII-Csp6I digested genomic DNA

value: Human wild-type Jurkat cells


title: female_F2_control_rep3 (4w)

source_name: F2 descendant of the control lineage


title: male_F3_test_rep3 (4z)


title: male_F2_test_rep4 (b)

source_name: F2 descendant of the test lineage


title: female_F1_test_rep1 (f4a)


title: male_F2_control_rep4 (a)


title: 4C-seq_Jurkat-WT_TLX3-promoter

description: DpnII-Csp6I digested genomic DNA


title: 4C-seq_DND-41_BCL11B-promoter

description: DpnII-Csp6I digested genomic DNA

value: Human DND-41 cells


title: male_F3_control_rep3 (3z)


title: female_F3_test_rep1 (4l4)


title: 4C-seq_DND-41_TLX3-promoter

description: DpnII-Csp6I digested genomic DNA


title: female_F3_control_rep2 (3y)


title: 4C-seq_Jurkat-SV_DMSO_TLX3-promoter_rep1

description: DpnII-Csp6I digested genomic DNA


title: male_F1_test_rep1 (f11)


title: female_F2_test_rep2 (4v)


title: male_F1_control_rep1 (f14.2)


title: female_F2_control_rep1 (4u)


title: male_F3_test_rep1 (3l4)


title: male_F2_control_rep1 (3u)


title: 4C-seq_UT242_BCL11B-promoter

description: DpnII-Csp6I digested genomic DNA

value: leukemia cells


title: female_F2_control_rep2 (3v)


title: ChIP-seq_Jurkat_input

data_processing:
Raw reads were aligned to human (hg19)  genome assembly using Bowtie2  with -k 1.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The bigwig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Assembly: hg19
Supplementary files format and content: bigwig file

source_name: Human Jurkat cells

growth_protocol: All the leukemia cells were cultured in RPMI supplemented with 20% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext Ulta II DNA Library Prep kit following the manufacturer’s protocol (New England Biolabs).

tag: chip antibody

value: Human Jurkat cells


title: 4C-seq_UT242_TLX3-promoter

description: DpnII-Csp6I digested genomic DNA


title: ChIP-seq_Jurkat_TLX3


title: male_F1_test_rep3 (30)


title: ChIP-seq_DND-41_input_rep2


title: female_F2_test_rep3 (3w)


title: female_F3_test_rep2 (4y)


title: female_F3_control_rep3 (2z)


title: ChIP-seq_DND-41_input_rep1


title: ChIP-seq_DND-41_MYB_rep2


title: 4C-seq_UT308_BCL11B-promoter

description: DpnII-Csp6I digested genomic DNA


title: male_F2_control_rep2 (2v)


title: ChIP-seq_DND-41_TLX3_rep2


title: male_F3_test_rep2 (2y)


title: male_F1_test_rep3 (31)


title: ChIP-seq_DND-41_MYB_rep1


title: female_F2_test_rep1 (2u)


title: ChIP-seq_UT308_input

source_name: leukemia patients

tag: cell type


title: ChIP-seq_DND-41_TLX3_rep1


title: female_F3_control_rep1 (2l4)


title: ChIP-seq_UT308_H3K27ac


title: male_F1_test_rep3 (28)


title: male_F1_test_rep3 (29)


title: ChIP-seq_UT242_input


title: ChIP-seq_UT242_H3K27ac


title: female_F1_test_rep3 (27)


title: ATAC-seq_DND-41_rep2

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
The bigwig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Assembly: hg19
Supplementary files format and content: bigwig files

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation.


title: ATAC-seq_LOUCY

source_name: Human LOUCY cells

value: Human LOUCY cells


title: female_F1_test_rep3 (26)


title: female_F1_test_rep3 (25)


title: ATAC-seq_Jurkat-SV_rep2

source_name: Human SV-engineered Jurkat cells


title: female_F1_test_rep3 (24)


title: ATAC-seq_DND-41_rep1


title: male_F2_test_rep3 (2w)


title: ATAC-seq_Jurkat-SV_rep1


title: male_F0_test_rep3 (22)


title: female_F0_test_rep3 (20)


title: ATAC-seq_Jurkat-WT_rep2

source_name: Human wild-type Jurkat cells


title: female_F3_test_rep3 (1z)


title: ATAC-seq_Jurkat-WT_rep1


title: male_F3_control_rep2 (1y)


title: PROseq_Lymphblastoid cells_D21_42C_rep2

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

description:
Eric_D21
nascent RNA (PRO-seq)

data_processing:
Library strategy: PRO-seq
PRO-seq data was processed using the Nascent-Flow pipeline (https://github.com/Dowell-Lab/Nascent-Flow) version 1.3 with the following flags: --flip, --genomeid ‘hg38’, --singleEnd, --fstitch --dastk --tfit --saveBAM.
In short, this pipeline mapped reads to GRCh38 with HISAT2 version 2.1.0 with the following flags: --very-sensitive, and --no-spliced-alignment. Sam files were converted to bam files using SAMtools version 1.8, and Picard Tools version 2.6.0 was used to identify duplicate reads and deduplicate. Bedtools version v2.28.0 was used to produce bedgraph files. The quality control programs FastQC version v0.11.8, preseq version 2.0.3, RSeqQC version 3.0.0, and Pileup from the BBMap Suite version 38.05 were run on the data. Peaks of active transcription were called using the FStitch program version 1.1. IGVtools version 2.3.75 was used to convert bedgraphs to tdf files.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bedgraphs supplied for PRO-seq libraries.

source_name: lymphoblastoid-EBV immortalized

growth_protocol: Cell lines were given pseudonyms Ethan and Eric for ease of use. Lymphoblastoid cells were grown in suspension in RPMI media supplemented with 20% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, and 2mM L-glutamine. Cell cultures were maintained in incubators with 5% CO2 at 37°C. Generally cells were grown in t25 or t75 flasks and split 1:10 every few days.

extract_protocol:
Nuclei isolations: Cells were grown in suspension in T75 [MAA1] flasks. After cell treatments, 10 ml aliquots of cells in media were washed 3X with cold PBS (phosphate buffer saline). Cells were next incubated on ice with buffer 1 containing 10 mM Tris pH 7.5, 2mM MgCl2, and 3 mM CaCl2 in DEPC (1% diethylpyrocarbonate treated) water, before centrifuging for 10 minutes at 1000 x G at 4°C. Buffer was then aspirated and cells were resuspended in 1ml of buffer 2 containing 10 mM Tris pH 7.5, 2mM MgCl2, and 3 mM CaCl2, 0.5% IGEPAL (octylphenoxy poly(ethyleneoxy)ethanol, branched, a nontoxic NP40 alternative), 10% glycerol, 2U/ml of SUPERase-IN, 1X protease inhibitor cocktail, and 1mM DTT (dithiothreitol) in DEPC treated water. After resuspension, 9 ml more of buffer 2 was added, samples were mixed by inverting the tube, and samples were then centrifuged for 10 minutes at 1000xG at 4°C. Solution was then aspirated, leaving behind cell nuclei. Nuclei were cleaned up by repeating the process of resuspending in 1ml of buffer 2, bringing solution up to 10 ml total buffer 2, spinning samples at 1000xG for 1 minutes, and aspirating media. White nuclei pellets were then resuspended in 1ml of buffer 3 containing 50 mM Tris pH 8.3, 5 mM MgCl2, 40% glycerol, and 0.1 mM EDTA (ethylenediaminetetraacetic acid) pH 8.0 in DEPC treated water. Nuclei in buffer 3 were transferred to pre-lubricated 1.7ml tubes, centrifuged for 5 minutes at 600xG at 4°C, and aspirated. Nuclei pellets were then resuspended in 500 ul of buffer 3, the centrifugation process was repeated, and final nuclei pellets were suspended in 110 ul buffer 3. A 1 ul aliquot of nuclei suspensions was diluted in PBS for nuclei quantification. Samples were diluted to make 100ul aliquots of 10 million nuclei each, and then flash frozen in liquid nitrogen and stored at -70°C.
Precision run on sequencing experiments (PRO-seq) were carried out according to the PRO-seq protocol (Mahat et al). ~10 million nuclei were used per sample. Prior to the run on experiment, Drosophila S2 cell line nuclei were spiked into each sample at approximately 1% for potential use in normalizing samples. Run on buffer containing 25 uM biotinylated rCTP, 25 uM rCTP, and 125 mM rATP, rGTP, and rUTP was used. Ampure bead cleanups were conducted at 1:1 ratios on the samples before and after the final PCR cleanup step.

treatment_protocol: Control 37C flasks were kept in incubator, while heat shock 42C flasks were floated in an external 42C waterbath for 1 hour prior to harvesting.

value: lymphoblastoid

value: disomic

value: 42C 1 hour heat shock


title: PROseq_Lymphblastoid cells_T21_37C_rep2

description:
Ethan_T21
nascent RNA (PRO-seq)

value: chromosome 21 trisomic

value: untreated (37C incubator)


title: PROseq_Lymphblastoid cells_D21_37C_rep2

description:
Eric_D21
nascent RNA (PRO-seq)


title: male_F2_control_rep3 (1w)

value: male


title: male_F1_control_rep3 (19)


title: male_F2_test_rep1 (1u)

value: test


title: PROseq_Lymphblastoid cells_T21_42C_rep1

description:
Ethan_T21
nascent RNA (PRO-seq)


title: male_F2_test_rep2 (1v)


title: female_F1_control_rep3 (18)

value: female

value: control


title: PROseq_Lymphblastoid cells_D21_37C_rep1

description:
Eric_D21
nascent RNA (PRO-seq)


title: PROseq_Lymphblastoid cells_D21_42C_rep1

description:
Eric_D21
nascent RNA (PRO-seq)


title: ATACseq_Lymphblastoid cells_T21_42C_rep2_technical2

description:
Ethan_T21
genomic DNA (ATAC-seq)
Ethan42merged_peaks_clean.narrowPeak

data_processing:
ATAC-seq data was processed using the ChIP-Flow pipeline (https://github.com/Dowell-Lab/ChIP-Flow) version 1.0.
In short, this pipeline trimmed reads with BBDuk version 38.05 with the following settings: ktrim=r, qtrim=10, k=23, mink=11, hdist=1, maq=10, minlen=20. Reads were mapped to GRCh38 with HISAT2 version 2.1.0 with the following settings: --very-sensitive, --no-spliced-alignment. Sam files were converted to bam files using SAMtools version 1.8, and Picard Tools version 2.6.0 was used to identify duplicate reads and deduplicate. BEDtools version v2.28.0 was used to produce bedGraph files from bam files. IGV Tools version 2.3.75 was used to produce TDF files from bedgraphs. For quality control of libraries, the QC programs FastQC version v0.11.8, preseq version 2.0.3, RSeQC version 3.0.0, and Pileup from the BBMap Suite version 38.0 were used.
Peak calling ATAC-seq: MACS2 version 2.1.1 was used to call peaks (callpeak) with the following settings: --SPMR, -q 0.0001. The genomic DNA preparations were used as control samples for peak calling (-c controlbams). Peak calling using MACS was carried out on the full bam files for ATAC-seq runs, as well as repeated on bam files with Chr21, ChrEBV, and ChrM removed for all downstream MuMerge and TFEA analyses used to compare data directly between different cell lines. Bedtools version 2.25.0 was used to remove blacklist regions from the resulting peak files using the bedtools intersect command with the Encode consensus blacklist regions. All downstream analysis using MACs2 peaks used the ‘narrowPeak’ files.
As noted above: For the second replicate of experiments, two sets of technical replicates were prepared for each condition. These replicates were carried out on cells from separate wells of a plate, but the cells were from the same cell lineages and passage numbers, so at the level of bam files, these technical replicates were merged into a single file, to be used as one cohesive second replicate of data.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bedgraphs and bed peak files supplied for ATAC-seq.

extract_protocol:
Suspension cells were then used to prepare an ATAC-seq library using the OMNI-ATAC-seq protocol. For control samples in calling ATAC-seq peaks, genomic DNA was extracted from each of the two cell lines using the Purelink genomic mini kit, then the genomic DNA was prepared for sequencing by carrying out the OMNI-ATAC protocol on this genomic DNA suspension.
For ATAC-seq, samples were pooled, size selected from 100-1000bp by blue pippen, SPRI bead cleaned up, and sequenced on a Nextseq V2 high output 75-cycle kit paired end 2x37 reads with dual 8bp indexes. For the second replicate of experiments, two sets of technical replicates were prepared for each condition. These replicates were carried out on cells from separate wells of a plate, but the cells were from the same cell lineages and passage numbers, so at the level of bam files, these technical replicates were merged into a single file, to be used as one cohesive second replicate of data.

treatment_protocol: The control 37C flasks were kept in incubator, while heat shock 42C flasks were floated in an external 42C waterbath for 1 hour prior to harvesting. For replicate 1 data, 1ml of each cell suspension containing approximately 50,000 cells was aliquoted into a 24 well tissue culture plate prior to the experiment. 1 plate of cells was then floated on a 42C waterbath for 1 hour, as the other control 37C plate remained in the cell incubator. 50 minutes into the heat shock/control treatment, all cell plates were collected and 2ul of DMSO was added to all samples before putting the control plate back in incubator and heat shock plate back in 42C waterbath. (The DMSO was a control for an unpublished experiment). After full hour of heat shock treatment has elapsed, both plates of cells were collected and placed on ice before spinning cells down and harvesting for ATAC-seq. For second replicate, heat shock or control treatment was carried out similarly but with approximately 30,000 cells per 1ml media in each 24 well plate well, and no DMSO was added during the experiment. For the second replicate of experiments, frozen S2 cells were spiked into the cell suspensions at approximately 1% after harvesting the cells but prior to the ATAC-seq experiment.


title: monkey M8020, xenograft biopsy tissue sample after xenotransplantation, day 184, TR2 [scRNA-Seq]

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

description: 10X Genomics

data_processing:
ENSEMBL Sscrofa11.1 FASTA assembly and v105 GTF annotation were prepared as a reference by removing unplaced contigs/scaffolds, and then adding intended genetic alterations/payload sequences as a separate contig. ENSEMBL Macaca fascicularis 6.0 FASTA assembly and v105 GTF annotations with unplaced contigs/scaffolds removed were appended to the pig reference for aligning reads from samples with expected NHP transcripts. Assembly construction and annotation was as described for bulk RNA-seq and was indexed here using STARsolo (2.7.9a) genomeGenerate on standard settings.
10X 3’ scRNA-seq was quantified using custom settings for STARsolo –soloCellFilter EmptyDrops_CR, --soloMultiMappers EM, --clipAdapterType CellRanger4, --outFilterScoreMin 30, --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts, --soloType Gene, --soloUMIdedup 1MM_CR, --soloUMIfiltering MultiGeneUMI_CR, and –soloUMIlen 12.
Counts were read into R (4.2.0) with DropletUtils (1.14.2) and cell quality checking and control performed using a set of filtering criteria: number of unique UMIs, detected features, %mitochondrial UMI, %protein-coding and lncRNA UMIs, complexity, and doublet removal using scDblFinder (1.8.0).
Count normalization was performed using scran (1.22.1) per recommendations for quickCluster, computerSumFactors, and logNormCounts. Cell-cycle analysis and annotation was performed with Seurat’s (4.1.0) CellCycleScoring. scVI was used to model and remove batch effect using covariates: %mitochondrial UMI, Seurat Cell Cycle S and G2M phase scores, and pig donor identification.  The 20 latent dimensions from scVI were passed to scran’s clusterCells and clustering performed using the bluster Louvain algorithm on shared nearest neighbors (v1.4.0; k=3; https://www.bioconductor.org/packages/release/bioc/html/bluster.html).
Uniform manifold approximation and projection (UMAP) was created via scater’s (1.22.0) runUMAP with 35 nearest neighbors and minimum distance 0.3. Cell types were assigned comparing known markers and the molecular signature database cell type signature enrichment from fgsea (v1.20.0; for a function on top 50 features per cell cluster) against cluster marker genes from scran’s scoreMarkers. UMAP plots were generated using scater’s ggcells and ggplot2 (3.2.0).
Assembly: ENSEMBL Sscrofa11.1 and ENSEMBL Macaca fascicularis 6.0
Supplementary files format and content: Archive of STARsolo outputs including raw count matrix in matrix market format, and barcodes and features in tab delimited format. An R RDS file containing a single cell experiment with the raw and normalized gene counts, as well as sample metadata.

organism: Sus scrofa

source_name: Cortex

extract_protocol:
Dissociation of kidney samples into single cell suspensions was performed using dissected cortex from necropsy and CUK samples or else from approximately 50% of a biopsy sample. Tissue pieces were minced into 1-2mm3 and digested by type IV collagenase (Sigma, C5138-500mg; 1mg/mL in 10mL of HBSS [ThermoFisher, MT-20023CV]). The resulting single cell suspensions were passed through a 100 m cell strainer (Miltenyi Biotec, 130-098-463), centrifuged and then passed through a 70 m cell strainer (Miltenyi Biotec, 130-098-462) and centrifuged again. RBC lysis was performed by resuspending these pellets with 4 mL RBC lysis buffer (Roche, 11814389001) and placed on ice for 2 minutes. RBC lysis reaction was quenched with 25mL 20% fetal bovine serum in HBSS and subsequently centrifuged again, pellets resuspended in HBSS and refiltered through 70 m filters. A dead cell removal step was performed using Dead Cell Removal Kit following the manufacturer’s instructions (Miltenyi Biotec, 130-090-101).
After dead cell removal, cells were counted and resuspended at ~600-1200cells/ L. These suspensions were applied to the 10X Genomics Chromium Next GEM Single Cell 3’ v3.1 kit to prepare scRNA-seq libraries, per manufacturer’s instructions (10X Genomics, 1000121).

value: Kidney

value: Cortex

value: Yucatan minipig

value: 184 days post-operative


title: monkey M4321, xenograft biopsy tissue sample after xenotransplantation, day 65, TR2 [scRNA-Seq]

description: 10X Genomics

value: 65 days post-operative


title: monkey M8020, xenograft biopsy tissue sample after xenotransplantation, day 184, TR1 [scRNA-Seq]

description: 10X Genomics


title: monkey M4321, xenograft biopsy tissue sample after xenotransplantation, day 65, TR1 [scRNA-Seq]

description: 10X Genomics


title: pig 21140, contralateral kidney medulla sample at day0/procurement, TR2 [scRNA-Seq]

description: 10X Genomics

source_name: Medulla

value: Medulla


title: male_F3_control_rep1 (1l4)


title: ATACseq_Lymphblastoid cells_T21_42C_rep2_technical1


title: pig 21140, contralateral kidney medulla sample at day0/procurement, TR1 [scRNA-Seq]

description: 10X Genomics


title: PROseq_Lymphblastoid cells_T21_42C_rep2

description:
Ethan_T21
nascent RNA (PRO-seq)


title: ATACseq_Lymphblastoid cells_T21_37C_rep2_technical1

description:
Ethan_T21
genomic DNA (ATAC-seq)
Ethan37merged_peaks_clean.narrowPeak


title: ATACseq_Lymphblastoid cells_T21_37C_rep2_technical2


title: female_F3_control_rep4 (xcf)


title: Zebrafish_melanoma_CDK13_R860Q_3pSeq_rep2

description: RNA 3' end sequencing

data_processing:
Mapped using STAR aligner version 2.7.2a (Dobin et al., 2013)
Custom Python script to filter reads from each bam file based on the following parameters: 1) Proper mate pairing; 2) orientation of the putative 3’ cleavage end corresponding to the direction of transcription for the gene to which reads mapped; 3) concordant mapping to known chromosomes; 4) no soft clippings; 5) skipped regions must be longer than 70 nucleotides.
Bedtools cluster tool version 2.26.0 (Quinlan and Hall, 2010) and custom Python scripts were used to generate read clusters by grouping any 3’ end coordinates that fell within 40 nucleotides of one another into a single cluster.
Clusters present in >1 replicate were considered to be true termination sites (high confidence termination sites). High confidence termination site reads were reclusters to define a complete and non-redundant 3' cleavage map for all conditions.
3' cleavage site reads were quantified using DEX-seq (Anders et al, 2012).
Assembly: GRCz11
Supplementary files format and content: 3pSeq counts tables contain gene coordinates, a unique polyA-site identifier, strand, and read counts

organism: Danio rerio

source_name: melanoma

growth_protocol: Melanomas generated from CDK13R860Q (n=3) or EGFP (n=3) injected into p53-/-; mitfa:BRAFV600E; mitfa-/- zebrafish were isolated and approximately equal cell numbers were gathered.

extract_protocol:
Poly-A selection was undertaken (NEB, E7490). Tissue was disrupted (Qiagen, 79654), DNA was removed, and RNA was isolated (Qiagen, 741134).
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina, 016.24

value: melanoma

value: CDK13R860Q injection


title: Zebrafish_melanoma_CDK13_R860Q_3pSeq_rep3

description: RNA 3' end sequencing


title: pig 21140, contralateral kidney cortex sample at day0/procurement, TR2 [scRNA-Seq]

description: 10X Genomics


title: Zebrafish_melanoma_CDK13_R860Q_3pSeq_rep1

description: RNA 3' end sequencing


title: female_F3_test_rep4 (xtf)


title: female_F1_test_rep2 (n12.1)

value: cyo/+; ser/+


title: Zebrafish_melanoma_eGFP_3pSeq_rep3

description: RNA 3' end sequencing

value: eGFP injection


title: pig 21140, contralateral kidney cortex sample at day0/procurement, TR1 [scRNA-Seq]

description: 10X Genomics


title: PROseq_Lymphblastoid cells_T21_37C_rep1

description:
Ethan_T21
nascent RNA (PRO-seq)

value: lymphoblastoid


title: Zebrafish_melanoma_eGFP_3pSeq_rep1

description: RNA 3' end sequencing