title: WT_p2hNCC_TFAP2A_6p24BP_inv


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_G03_S75_comb

status: Public on Nov 01 2018

type: SRA

city: Cambridge

first: Orr

last: Ashenberg

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

institute: Broad Institute

description:
Full-length RNAseq (SMART-Seq2) reads.
processed data file: counts.csv
processed data file: tpm.csv
processed data file: cell.annotations.csv

library_source: transcriptomic

data_processing:
Full-length RNAseq (SMART-Seq2).
Tophat
Bowtie mapping to UCSC hg19 human transcriptome.
RSEM v1.2.8
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: cell.annotations.csv: Comma-separated cell sample annotation table; For each cell (row): cell name, sample type, cell type, treatment group, cohort, number of genes, number of reads.
Supplementary_files_format_and_content: counts.csv: Comma-separated counts table; Full-length RNAseq (SMART-Seq2); The expression levels for each gene (rows) in each single cell (column) in counts as calculated using RSEM.
Supplementary_files_format_and_content: tpm.csv: Comma-separated log-transformed transcripts per million (TPM) table; Values are provided as log2[(TPM/10) +1]; Full-length RNAseq (SMART-Seq2); The expression levels for each gene (rows) in each single cell (column) in transcripts per million (TPM) as calculated using RSEM.

molecule: total RNA

organism: Homo sapiens

source_name: melanoma tumor

extract_protocol:
Dissociated individual cells from fresh tumor resections. Isolated immune and non-immune cells by FACS based on CD45 staining.
Full-length RNAseq (SMART-Seq2) libraries sequenced with 38bp paired-end reads on an Illumina NextSeq 500.

tag: tumor-of-origin

tag: treatment-group

tag: cohort

value: Tirosh

tag: cell type

value: Mal


title: CY88_3_G07_S655_comb


title: cy78_CD45_neg_3_B08_S692_comb


title: HA 1 - Unstim

city: Epalinges

first: Sylvain

last: Perriot

state: Vaud

address: Chemin des Boveresses 155, Building CLEC / Room C203

country: Switzerland

institute: CHUV

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 2.20.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Homo sapiens (build GRCh38) genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Homo sapiens  gene annotation (build GRCh38, Ensembl v. 92).
Genome_build: Homo sapiens build GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: Fetal primary astrocytes

growth_protocol: DMEM/F-12 medium supplemented with B-27 supplement without vitamin A, cells were plated on matrigel

extract_protocol:
RNeasy plus mini kit
RNA-seq libraries were prepared using 100-200ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Caliper Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a Caliper-developed automated script.

treatment_protocol: 24hrs stimulation

tag: donor/origin

value: Fetal brain

tag: stimulation

value: Fetal primary astrocytes


title: HA 1 - FBS

value: Fetal bovine serum


title: HA 2 - Unstim


title: HA 3 - FBS


title: HA 3 - Unstim


title: HA 2 - FBS


title: cy81_Bulk_CD45_neg_C04_S124_comb


title: Cy81_FNA_CD45_B11_S311_comb


title: MS 3 - IL-6

source_name: hiPSC-derived astrocytes

value: MS patient 3

value: hiPSC-derived astrocytes


title: MS 3 - TNFa+IL-1b


title: cy80_CD45_neg_E01_S913_comb


title: Cy81_Bulk_CD45_B12_S120_comb


title: Ly/CD8b+/CLA-/ITGB7- T cells_aGvHD developed: Absent_Patient No. 1

type: RNA

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: Batch 3

hyb_protocol: Cy3-labeled amplified cRNA was hybridized to human GE 4x44K v2 whole-genome microarrays (Agilent) and scanned on an Agilent Microarray Scanner. Raw data were retrieved with the Feature Extraction software (Agilent

scan_protocol: Samples were scanned on an Agilent Microarray Scanner.

data_processing: Batch effect was removed by distance weighted discrimination. Analyses were performed using BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team. All genes flagged as not detected, displaying batch adjusted signal intensities lower than log2=1, not detected in all samples of any experimental groups, or not displaying 2-fold change in at least one experimental group in either direction from the gene’s median value, were censored. The remaining gene set (1981 genes) was analyzed by Two-way repeated measures ANOVA and Benjamini-Hochberg multiple testing correction (FDR<0.01) to identify differentially expressed genes (DEGs).

source_name: Peripheral blood

label_protocol: Sample integrity and yield were assessed on a 2100 Bioanalyzer using an RNA 6000 Pico Kit. Three thousand pg total RNA per sample was amplified in two rounds and Cy3-labeled by the Arcturus RiboAmp HS PLUS, Cy3 labeling Kit.

growth_protocol: Blood samples were collected from 20 selected allo-HSCT patients of the Dept. of Hematology and Stem Cell Transplantation, St. Istvan and St Laszlo Hospital, Budapest, Hungary for research purposes, with informed consent and IRB approval. Patients were recruited to create four age- and gender-matched groups that developed no acute GvHD, acute cutaneous GvHD, acute gastrointestinal GvHD, or both acute and gastrointestinal GvHD after allo-HSCT (n=5 each). Samples were collected at the time of diagnosis before any GvHD-specific treatment had been commenced with (GvHD groups), or around day 30 post allo-HSCT (no-GvHD group)

extract_protocol: Cells were sorted directly into RLT Plus lysis buffer. Total RNA was isolated using an RNEasy Plus Micro kit.

treatment_protocol: Peripheral blood was collected using Acid Citrate Dextrose (ACD-A) tubes. PBMCs were isolated by density centrifugation, and stained with LIVE/DEAD® Fixable Dead Cell Stain Near-IR (Thermo), anti-human CD8β-APC, anti-human Cutaneous Lymphocyte Antigen (CLA)-FITC, and anti-human Integrin β7 (ITGB7)-PE antibodies. Three-way sorting of PBMCs was done on a BD FACSAria III sorter. Skin-homing LIVE/DEAD®-/CD8b+/CLA+ T cells, gut-homing LIVE/DEAD®-/CD8b+/ITGB7+ T cells, and LIVE/DEAD®-/CD8b+/CLA-/ITGB7- T cells, the latter serving as reference, were acquired with help of the FACSDiva software (BD).

tag: agvhd developed

value: Absent

tag: t cell subset

tag: patient no.


title: Cy80_II_CD45_B02_S878_comb


title: MS 3 - TNFa

value: TNFa


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_B10_S310_comb


title: MS 3 - Unstim


title: MS 1 - FBS

value: MS patient 1


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_G12_S180_comb


title: MS 1 - IL-6


title: Cy81_Bulk_CD45_C06_S126_comb

value: Undetermined


title: MS 3 - FBS


title: cy78_CD45_neg_1_C10_S514_comb


title: cy81_Bulk_CD45_neg_C08_S128_comb


title: MS 1 - IL-1b


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_G07_S79_comb


title: MS 3 - IL-1b


title: HC 3 - IL-6

value: Health donor 3


title: HC 3 - TNFa+IL-1b


title: MS 1 - Unstim


title: cy78_CD45_neg_3_D09_S717_comb


title: Cy81_FNA_CD45_H10_S382_comb


title: HC 3 - IL-1b


title: cy78_CD45_neg_1_G04_S556_comb


title: HC 3 - FBS


title: MS 2 - IL-6

value: MS patient 2


title: Cy71_CD45_H10_S574_comb


title: MS 1 - TNFa


title: cy53_1_CD45_neg_H12_S384_comb


title: cy82_CD45_pos_2_E07_S535_comb


title: HC 3 - Unstim


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_G04_S172_comb


title: MS 2 - FBS


title: cy79_p5_CD45_neg_PDL1_neg_G03_S843_comb


title: MS 2 - TNFa+IL-1b


title: cy78_CD45_neg_2_C05_S605_comb


title: cy79_p4_CD45_neg_PDL1_pos_A08_S392_comb


title: cy79_p4_CD45_neg_PDL1_pos_D12_S432_comb


title: MS 1 - TNFa+IL-1b


title: cy80_CD45_neg_H02_S950_comb


title: HC 3 - TNFa


title: cy53_1_CD45_neg_E12_S348_comb


title: MS 2 - TNFa


title: cy78_CD45_neg_1_D05_S521_comb


title: MS 4 - FBS

value: MS patient 4


title: MS 2 - Unstim


title: cy80_CD45_neg_H09_S957_comb


title: cy79_p5_CD45_neg_PDL1_neg_C09_S801_comb


title: CY88_5_E02_S722_comb


title: MS 4 - IL-6


title: cy79_p5_CD45_neg_PDL1_neg_G09_S849_comb


title: MS 4 - IL-1b


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_B07_S115_comb


title: MS 4 - TNFa+IL-1b


title: HC2 - FBS

value: Health donor 2


title: Cy81_FNA_CD45_B10_S310_comb


title: cy80_CD45_neg_A03_S867_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_H07_S187_comb


title: MS 4 - TNFa


title: cy79_p5_CD45_pos_PD1_pos_E02_S626_comb


title: MS 2 - IL-1b


title: HC2 - TNFa+IL-1b


title: HC2 - TNFa


title: cy79_p5_CD45_neg_PDL1_neg_H07_S859_comb


title: HC2 - Unstim


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_F03_S63_comb


title: cy79_p5_CD45_neg_PDL1_pos_E08_S728_comb


title: HC 1 - IL-6

value: Health donor 1


title: HC 1 - FBS


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_C08_S128_comb


title: HC 1 - TNFa+IL-1b


title: cy79_p4_CD45_neg_PDL1_pos_C12_S420_comb


title: HC 1 - IL-1b


title: HC 1 - TNFa


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_F04_S160_comb


title: MS 4 - Unstim


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_B04_S304_comb


title: HC2 - IL-6


title: cy79_p5_CD45_neg_PDL1_pos_E03_S723_comb


title: cy78_CD45_neg_3_D08_S716_comb


title: cy80_CD45_neg_C09_S897_comb


title: Cy71_CD45_G09_S561_comb


title: Cy71_CD45_F11_S551_comb


title: cy79_p5_CD45_neg_PDL1_neg_H10_S862_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_A12_S108_comb


title: cy80_CD45_neg_D07_S907_comb


title: CY88_3_C08_S608_comb


title: UCI_06_DLPFC

city: Irvine

first: Brooke

middle: E.

last: Hjelm

state: CA

address: 837 Health Sciences Rd

department: Department of Psychiatry and Human Behavior

institute: University of California, Irvine

description: mtDNA (long-range PCR)

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Illumina software used for basecalling, bcl2fastq conversion and demultiplexing.
We removed PCR replicates and reads that mapped to the TruSeq adapter sequence prior to alignment using the BBTools suite (BBMap v.35.14).
Paired-end fastq files were aligned to the rCRS (revised Cambridge Reference Sequence (rCRS); version NC_012920.1) reference FASTA file using MapSplice (v2.1.8).
Aligned SAM/BAM files were further processed using Picard tools (v.1.96), Samtools (v.1.8), and Python (v.2.7) for determination of Benchmark coverage values (used for normalization). See Splice-Break methods paper for details.
Putative mtDNA deletion breakpoints (located in junctions.txt file from alignment output) were further filtered to remove reads with a low overhang, those proximal (within 500bp) to the primers, and most singleton calls. See Splice-Break methods paper for details. Finalized catalogue contains 4,489 mtDNA deletion breakpoints.
Genome_build: NC_012920.1
Supplementary_files_format_and_content: Splice-Break_4489x93_deletion_matrix.txt: Matrix file of 4,489 mtDNA deletion breakpoints x 93 samples; units shown are in % after normalization to Benchmark coverage.
Supplementary_files_format_and_content: deletion-metadata-SAMPLE.txt: Cumulative mtDNA deletion metrics and Benchmark coverage for each individual sample. See Splice-Break methods paper for details.

molecule: genomic DNA

source_name: Dorsolateral prefrontal cortex (DLPFC)

extract_protocol:
Approximately 50mg of pulverized brain tissue (grey matter only), or 50μl of frozen whole blood, was used for DNA extraction. Total DNA from brain tissue was extracted using the DNeasy Blood & Tissue Kit (Cat# 69504 or 69506, Qiagen), or the AllPrep DNA/RNA/Protein Kit (Qiagen, Valencia, CA, USA). For blood samples, DNA was isolated using 50μl of frozen whole blood (that had been stored in EDTA blood collection tubes) using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA).
Long-range PCR protocol: Prior to NGS library preparation, the mtDNA was enriched for each sample using a 30-cycle long-range (LR) PCR that utilizes back-to-back primers that hybridize to the control region of the mitochondrial genome. Primer sequences used were 5’-CCGCACAAGAGTGCTACTCTCCTC-3’ and 5’-GATATTGATTTCACGGAGGATGGTG-3’ (Integrated DNA Technologies, Coralville, IA, USA), for the forward and reverse primers, respectively. PCR products then were purified using Agencourt AMPure XP beads (Beckman Coulter, Indianapolis, IN, USA).
Fragmentation (Covaris) protocol: DNA shearing performed in S220 Covaris microTUBEs with the following settings: Duty Factor=5%, Peak Incident Power=175 W, Cycles per Burst=200, Time=35 s.
Libraries were prepared using the TruSeq Nano DNA HT Library Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Each library was barcoded so that samples could be multiplex sequenced together with 96 samples per lane.

tag: subject id

tag: psych dx

value: Schizophrenia (SZ)

tag: age (yrs)

tag: Sex

value: Male

tag: tissue

value: Dorsolateral prefrontal cortex (DLPFC)

tag: mtdna deletion outlier

value: no


title: UCI_08_BLOOD

description: mtDNA (long-range PCR)

source_name: Whole blood (BLOOD)

value: Female

value: Whole blood (BLOOD)


title: UCI_07_BLOOD

description: mtDNA (long-range PCR)


title: UCI_07_DLPFC

description: mtDNA (long-range PCR)


title: UCI_09_BLOOD

description: mtDNA (long-range PCR)


title: UCI_08_DLPFC

description: mtDNA (long-range PCR)


title: HC2 - IL-1b


title: cy60_1_cd_45_neg_3_C10_S514_comb

value: Tirosh

value: Mal


title: UCI_06_BLOOD

description: mtDNA (long-range PCR)


title: UCI_05_DLPFC

description: mtDNA (long-range PCR)


title: HC 1 - Unstim

value: hiPSC-derived astrocytes


title: cy78_CD45_neg_1_F08_S548_comb


title: UCI_05_BLOOD

description: mtDNA (long-range PCR)


title: cy79_p4_CD45_neg_PDL1_neg_A03_S1059_comb


title: UCI_04_DLPFC

description: mtDNA (long-range PCR)


title: UCI_09_DLPFC

description: mtDNA (long-range PCR)


title: UCI_04_BLOOD

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_1_A03_S483_comb


title: Cy81_Bulk_CD45_B09_S117_comb


title: cy79_p5_CD45_neg_PDL1_neg_H06_S858_comb


title: UCI_03_HIPP

description: mtDNA (long-range PCR)

source_name: Hippocampus (HIPP)

value: Unaffected control (CTRL)

value: Hippocampus (HIPP)


title: UCI_03_PUT

description: mtDNA (long-range PCR)

source_name: Putamen (PUT)

value: Putamen (PUT)


title: cy82_CD45_pos_1_E08_S536_comb


title: cy80_CD45_neg_B01_S877_comb


title: UCI_03_DLPFC

description: mtDNA (long-range PCR)


title: UCI_03_CAUN

description: mtDNA (long-range PCR)

source_name: Caudate nucleus (CAUN)

value: Caudate nucleus (CAUN)


title: cy79_p5_CD45_neg_PDL1_neg_F05_S833_comb


title: UCI_03_BLOOD

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_3_D07_S715_comb


title: cy81_Bulk_CD45_neg_E09_S153_comb


title: UCI_03_ACC

description: mtDNA (long-range PCR)

source_name: Anterior cingulate cortex (ACC)

value: Anterior cingulate cortex (ACC)


title: cy88_cd45pos_5_C01_S217_comb


title: UCI_02_PUT

description: mtDNA (long-range PCR)


title: UCI_02_HIPP

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_1_B08_S500_comb


title: UCI_02_BLOOD

description: mtDNA (long-range PCR)


title: cy80_CD45_neg_D03_S903_comb


title: UCI_02_ACC

description: mtDNA (long-range PCR)


title: Cy71_CD45_D11_S527_comb


title: cy79_p5_CD45_neg_PDL1_neg_A05_S773_comb


title: UCI_01_PUT

description: mtDNA (long-range PCR)

value: Major depressive disorder (MDD)


title: UCI_01_HIPP

description: mtDNA (long-range PCR)


title: cy79_p4_CD45_neg_PDL1_neg_B11_S1079_comb


title: UCI_01_DLPFC

description: mtDNA (long-range PCR)


title: UCI_01_CAUN

description: mtDNA (long-range PCR)

value: yes


title: cy78_CD45_neg_3_G09_S753_comb


title: cy79_p4_CD45_neg_PDL1_neg_A12_S1068_comb


title: cy81_FNA_CD45_neg_E12_S1020_comb


title: Cy80_II_CD45_D09_S909_comb


title: SBB_32_DLPFC

description: mtDNA (long-range PCR)


title: UCI_01_ACC

description: mtDNA (long-range PCR)


title: SBB_32_ACC

description: mtDNA (long-range PCR)


title: cy79_p3_CD45_neg_PDL1_neg_B06_S210_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_F06_S162_comb


title: UCI_02_DLPFC

description: mtDNA (long-range PCR)


title: SBB_31_DLPFC

description: mtDNA (long-range PCR)


title: cy82_CD45_pos_3_C11_S35_comb

value: Undetermined


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_C04_S316_comb


title: SBB_31_ACC

description: mtDNA (long-range PCR)

value: Schizophrenia (SZ)


title: SBB_30_DLPFC

description: mtDNA (long-range PCR)

value: Alcohol, drug abuse, other (ADO)

value: Male


title: SBB_30_ACC

description: mtDNA (long-range PCR)

value: no


title: SBB_29_DLPFC

description: mtDNA (long-range PCR)

value: Bipolar disorder (BD)

value: Dorsolateral prefrontal cortex (DLPFC)


title: Cy80_II_CD45_G09_S945_comb

value: Tirosh


title: cy79_p5_CD45_neg_PDL1_pos_G05_S749_comb

value: Mal


title: cy79_p4_CD45_neg_PDL1_pos_C04_S412_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_F11_S167_comb


title: cy79_p4_CD45_neg_PDL1_neg_F03_S1119_comb


title: SBB_29_ACC

description: mtDNA (long-range PCR)


title: UCI_01_BLOOD

description: mtDNA (long-range PCR)

value: Whole blood (BLOOD)


title: SBB_28_DLPFC

description: mtDNA (long-range PCR)


title: SBB_28_ACC

description: mtDNA (long-range PCR)


title: cy81_FNA_CD45_neg_B04_S976_comb


title: SBB_27_ACC

description: mtDNA (long-range PCR)


title: SBB_27_DLPFC

description: mtDNA (long-range PCR)


title: SBB_26_DLPFC

description: mtDNA (long-range PCR)


title: CY88_3_C12_S612_comb


title: CY89FNAQ2_H03_S471_comb


title: SBB_26_ACC

description: mtDNA (long-range PCR)


title: SBB_25_DLPFC

description: mtDNA (long-range PCR)


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_H03_S375_comb


title: SBB_25_ACC

description: mtDNA (long-range PCR)


title: cy79_p4_CD45_neg_PDL1_pos_F06_S450_comb


title: CY89NEG_H06_S90_comb


title: cy79_p4_CD45_neg_PDL1_pos_D01_S421_comb


title: SBB_24_DLPFC

description: mtDNA (long-range PCR)


title: CY88_5_D10_S718_comb


title: SBB_23_DLPFC

description: mtDNA (long-range PCR)


title: SBB_24_ACC

description: mtDNA (long-range PCR)


title: cy60_1_cd_45_neg_3_F06_S546_comb


title: cy94_cd45neg_cd90pos_A11_S299_comb


title: cy79_p4_CD45_neg_PDL1_pos_D05_S425_comb


title: cy81_FNA_CD45_neg_F02_S1022_comb


title: SBB_22_ACC

description: mtDNA (long-range PCR)


title: CY88_3_B12_S600_comb


title: SBB_21_DLPFC

description: mtDNA (long-range PCR)


title: SBB_21_ACC

description: mtDNA (long-range PCR)


title: cy79_p4_CD45_neg_PDL1_pos_B11_S407_comb


title: cy79_p3_CD45_neg_PDL1_neg_B11_S215_comb


title: SBB_20_DLPFC

description: mtDNA (long-range PCR)

value: Female


title: CY88_5_D08_S716_comb


title: Cy81_Bulk_CD45_E08_S152_comb


title: Cy81_FNA_CD45_H12_S384_comb


title: cy79_p5_CD45_neg_PDL1_neg_G04_S844_comb


title: SBB_19_DLPFC

description: mtDNA (long-range PCR)


title: SBB_20_ACC

description: mtDNA (long-range PCR)


title: cy79_p3_CD45_neg_PDL1_neg_E05_S245_comb


title: SBB_18_ACC

description: mtDNA (long-range PCR)


title: SBB_18_DLPFC

description: mtDNA (long-range PCR)


title: SBB_17_DLPFC

description: mtDNA (long-range PCR)


title: CY88_5_H05_S761_comb


title: SBB_17_ACC

description: mtDNA (long-range PCR)


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_G02_S170_comb


title: SBB_23_ACC

description: mtDNA (long-range PCR)


title: Cy80_II_CD45_B09_S885_comb


title: cy79_p5_CD45_neg_PDL1_pos_G02_S746_comb


title: SBB_22_DLPFC

description: mtDNA (long-range PCR)


title: SBB_16_DLPFC

description: mtDNA (long-range PCR)


title: cy79_p5_CD45_neg_PDL1_pos_E10_S730_comb


title: SBB_15_DLPFC

description: mtDNA (long-range PCR)


title: CY89FNAQ2_C04_S412_comb


title: CY88_5_B12_S696_comb


title: CY88_3_H10_S670_comb


title: SBB_15_ACC

description: mtDNA (long-range PCR)


title: SBB_19_ACC

description: mtDNA (long-range PCR)


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_B11_S119_comb


title: SBB_14_ACC

description: mtDNA (long-range PCR)


title: cy79_p3_CD45_neg_PDL1_neg_D09_S237_comb


title: SBB_13_DLPFC

description: mtDNA (long-range PCR)


title: SBB_16_ACC

description: mtDNA (long-range PCR)


title: SBB_13_ACC

description: mtDNA (long-range PCR)


title: CY89FNAQ2_B02_S398_comb


title: SBB_12_DLPFC

description: mtDNA (long-range PCR)


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_A07_S7_comb


title: SBB_12_ACC

description: mtDNA (long-range PCR)


title: SBB_14_DLPFC

description: mtDNA (long-range PCR)


title: SBB_11_DLPFC

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_3_E05_S725_comb


title: SBB_11_ACC

description: mtDNA (long-range PCR)


title: cy81_FNA_CD45_neg_H09_S1053_comb


title: SBB_10_DLPFC

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_1_H04_S568_comb


title: SBB_10_ACC

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_1_F10_S550_comb


title: SBB_09_DLPFC

description: mtDNA (long-range PCR)


title: SBB_09_ACC

description: mtDNA (long-range PCR)


title: CY89CORE11_D09_S141_comb


title: cy79_p4_CD45_neg_PDL1_neg_H01_S1141_comb


title: Cy81_FNA_CD45_F02_S350_comb


title: SBB_07_DLPFC

description: mtDNA (long-range PCR)


title: cy79_p4_CD45_neg_PDL1_neg_B04_S1072_comb


title: SBB_08_ACC

description: mtDNA (long-range PCR)


title: CY89NEG_A06_S6_comb


title: SBB_07_ACC

description: mtDNA (long-range PCR)


title: Cy71_CD45_H06_S570_comb


title: SBB_06_ACC

description: mtDNA (long-range PCR)


title: cy79_p3_CD45_neg_PDL1_neg_C07_S223_comb


title: SBB_05_DLPFC

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_3_G07_S751_comb


title: CY89CORE11_B06_S114_comb


title: CY89CORE11_A05_S101_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_E08_S56_comb


title: SBB_04_DLPFC

description: mtDNA (long-range PCR)


title: SBB_05_ACC

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_1_F02_S542_comb


title: cy79_p4_CD45_neg_PDL1_pos_H11_S479_comb


title: cy79_p3_CD45_neg_PDL1_neg_H10_S286_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_F03_S159_comb


title: SBB_03_DLPFC

description: mtDNA (long-range PCR)


title: SBB_03_ACC

description: mtDNA (long-range PCR)


title: SBB_02_DLPFC

description: mtDNA (long-range PCR)


title: CY89CORE11_B04_S112_comb


title: SBB_08_DLPFC

description: mtDNA (long-range PCR)


title: cy78_CD45_neg_1_H08_S572_comb


title: SBB_06_DLPFC

description: mtDNA (long-range PCR)


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_H01_S373_comb


title: cy79_p4_CD45_neg_PDL1_pos_E10_S442_comb


title: SBB_01_DLPFC

description: mtDNA (long-range PCR)


title: SBB_02_ACC

description: mtDNA (long-range PCR)


title: SBB_01_ACC

description: mtDNA (long-range PCR)


title: R720:_iNSC-SC_MJD33b-1-II-10_day18_P21

city: Bonn

first: Andreas

last: Till

state: NRW

address: Sigmund-Freud-Str. 25

department: Institute of Reconstructive Neurobiology

country: Germany

institute: University of Bonn

description: RNA-Seq

data_processing:
Transcript and gene level quantification was performed using Salmon55 in combination with the human cDNA file for genome GRCh37 version 89 obtained from ENSEMBL. Gene level read counts were then further analysed in R using tximport and DESeq2. Prior to further analysis, mitochondrial genes, as well as genes with less than a total read count of 4 across all samples (40th percentile) and more than 17,488 reads (95th percentile) were removed. All data was normalized based on standard size factor estimates and variance stabilization transformation was performed on filtered data, giving rise to the normalized gene expression matrix.
Genome_build: GRCh37
Supplementary_files_format_and_content: ENSEMBL gnee ID and gene symbol ENSEMBL verison 89, variance stabilzation transformed gene level counts.

source_name: R720: iNSC-SC MJD33b-1-II-10 day18 P21

growth_protocol: For erythrocyte progenitor cell (EPC) preparation, peripheral blood was separated in CPT tubes (BD Vacutainer CPT) following the manufacturer’s protocol to isolate peripheral blood mononuclear cells. After 7 days, EPCs were purified by a Percoll density gradient (Sigma) after a method published by van den Akker et al (2010). Purified EPCs were expanded for another 2 days in expansion medium without IL-3. Cord blood (CB)-CD34+ cells were cultured for one day before infection in CBC medium.     For iNSC generation, erythroblasts and CB-CD34+ cells were infected with SeV expressing SOX2 and c-MYC (CytoTuneTM-iPS kit, ThermoFisher) at day 0. At day 1, infected cells were replated into dishes coated with matrigel (Corning) in iNSC-conversion medium. For initial experiments, infected cells were plated on mouse embryonic fibroblasts. Cultures were maintained under hypoxic conditions (37°C, 5 % O2, 5 % CO2). Single neuroepithelial colonies were manually picked between day 11 and day 21 and further expanded as single colony-derived iNSCs. Alternatively, neuroepithelial colonies were re-suspended using pre-warmed accutase (Life Technologies) and cultured as poly-colony-derived iNSCs. Single- and poly-colony-derived iNSCs were further propagated in matrigel-coated dishes in iNSC expansion medium. Cultures were switched back to normoxic conditions (37°C, 21 % O2, 6-9 % CO2) once iNSC colonies attached. After expansion for 7 - 10 passages, iNSCs were cultured at 39°C for about 3 - 4 weeks until the complete elimination of SeV vectors was confirmed by RT-PCR.    Generation of smNPCs from PB-iPSCs is based on a published protocol (Reinhardt et al, 2013).

extract_protocol:
RNeasy kit (QIAgen) standard procedure
QuantSeq 3’ mRNA seq Library Prep Kit (Lexogen)
3' RNA-Seq. Libraries were sequenced using the Illumina HiSeq 2500 platform.

treatment_protocol: no differential treatment

value: iNSC

tag: donor

tag: passage


title: cy79_p5_CD45_neg_PDL1_pos_F09_S741_comb

tag: tumor-of-origin


title: R909:_iNSC-SC_82b-1-SC_(EPC-1-II-1)_day11_P5

description: RNA-Seq


title: cy79_p4_CD45_neg_PDL1_pos_C02_S410_comb

tag: treatment-group


title: R913:_smNPC_MJD33b_P6

description: RNA-Seq

source_name: R913: smNPC MJD33b P6

value: smNPC


title: cy79_p4_CD45_neg_PDL1_neg_H09_S1149_comb

tag: cohort


title: cy79_p5_CD45_neg_PDL1_pos_C11_S707_comb

tag: cell type


title: Cy81_Bulk_CD45_G12_S180_comb


title: SBB_04_ACC

description: mtDNA (long-range PCR)


title: cy81_FNA_CD45_neg_F06_S1026_comb


title: R677:_iNSC-SC_82b-3-SC_(EPC-2-II-3)_day14_P21

description: RNA-Seq


title: cy80_CD45_neg_F05_S929_comb


title: CY89FNAQ2_G07_S463_comb


title: R867:_iNSC-SC_107b-2-II-3_day11_P21

description: RNA-Seq


title: R891:_iNSC-SC_MJD33b-2-II-3_day11_P6

description: RNA-Seq

source_name: R891: iNSC-SC MJD33b-2-II-3 day11 P6


title: CY88CD45POS_7_C07_S223_comb

value: Macrophage


title: R713:_smNPC_MJD33b_P18

description: RNA-Seq

source_name: R713: smNPC MJD33b P18


title: R910:_iNSC-SC_82b-1-SC_(EPC-1-II-1)_day11_P21

description: RNA-Seq


title: CY88_3_A10_S586_comb


title: R882:_iNSC-SC_MJD33b-2-V-8_day11_P21

description: RNA-Seq

source_name: R882: iNSC-SC MJD33b-2-V-8 day11 P21


title: R760:_EPC_iLB-C-107b

description: RNA-Seq

source_name: R760: EPC iLB-C-107b

value: EPC


title: cy79_p5_CD45_neg_PDL1_neg_C02_S794_comb


title: CY89NEG_E06_S54_comb


title: R908:_iNSC-PC_107b-PC_(JK80bm-1-II-PC)_day16_P3

description: RNA-Seq

source_name: R908: iNSC-PC 107b-PC (JK80bm-1-II-PC) day16 P3


title: cy79_p4_CD45_neg_PDL1_pos_A04_S388_comb

source_name: melanoma tumor


title: R877:_iNSC-SC_MJD33b-2-II-3_day11_P21

description: RNA-Seq

source_name: R877: iNSC-SC MJD33b-2-II-3 day11 P21


title: cy79_p4_CD45_neg_PDL1_pos_D03_S423_comb


title: cy80_CD45_neg_A05_S869_comb


title: R729:_EPC_iLB-MJD3-33bf

description: RNA-Seq

source_name: R729: EPC iLB-MJD3-33bf


title: R911:_smNPC_107b_P6

description: RNA-Seq

source_name: R911: smNPC 107b P6


title: R886:_iNSC-SC_MJD33b-1-II-10_day18_P5

description: RNA-Seq

source_name: R886: iNSC-SC MJD33b-1-II-10 day18 P5


title: CY89CORE11_E10_S154_comb


title: R885:_iNSC-SC_MJD33b-2-V-8_day11_P5

description: RNA-Seq

source_name: R885: iNSC-SC MJD33b-2-V-8 day11 P5


title: R705:_smNPC_107b_P18

description: RNA-Seq


title: R699:_iNSC-PC_107b-PC_(JK80bm-1-II-PC)_day16_P19

description: RNA-Seq

source_name: R699: iNSC-PC 107b-PC (JK80bm-1-II-PC) day16 P19


title: cy78_CD45_neg_1_A04_S484_comb


title: cy82_CD45_pos_2_B03_S495_comb


title: Cy80_II_CD45_B01_S877_comb


title: cy79_p5_CD45_neg_PDL1_pos_H06_S762_comb


title: cy79_p4_CD45_neg_PDL1_neg_F12_S1128_comb


title: R892:_iNSC-SC_107b-2-II-3_day11_P6

description: RNA-Seq


title: Cy81_FNA_CD45_C05_S317_comb


title: BNab_BDT060P4

city: Durham

first: Todd

last: Bradley

address: 2 Genome Court

institute: Duke University Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic.0.32
The clipped reads were mapped to the hg38 transcriptome using Bowtie2 v2.1.0
Expression quantification was done using express v1.5.1
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited text files include effective count values for each sample

molecule: polyA RNA

extract_protocol:
RNA was extracted using the Qiagen AllPrep DNA/RNA Mini kit (Qiagen;80204) following manufactures protocol
TruSeq stranded mRNA kit (Illumina)

tag: subject status

value: individuals that developed HIV-1 broadly neutralizing antibodies (BNab)

tag: country

value: USA:United Kingdom

tag: biological sex

tag: age at screening

value: Peripheral Blood

value: peripheral blood mononuclear cells (PBMC)

tag: rnaseq id


title: BNab_KDT060P8


title: Control_GDT082CY

value: Control

value: Tanzania


title: BNab_HDT00QLN


title: Control_EDT08


title: Cy81_Bulk_CD45_D10_S142_comb


title: Cy81_Bulk_CD45_D01_S133_comb

value: Undetermined


title: Control_JDT060P6


title: cy79_p3_CD45_neg_PDL1_neg_G03_S267_comb


title: cy81_Bulk_CD45_neg_E02_S146_comb

value: Endo.


title: Control_CDT0827R


title: BNab_DDT052LD


title: cy80_CD45_neg_H08_S956_comb


title: CY89NEG_F05_S65_comb


title: BNab_JDT052KT


title: BNab_EDT052L0


title: cy53_1_CD45_neg_B02_S302_comb


title: cy79_p3_CD45_neg_PDL1_neg_F08_S260_comb


title: BNab_DDT072V1


title: BNab_KDT033RB


title: CY89NEG_F07_S67_comb


title: cy79_p5_CD45_neg_PDL1_pos_C10_S706_comb


title: Cy71_CD45_F06_S546_comb


title: cy79_p5_CD45_neg_PDL1_pos_A11_S683_comb


title: Control_BDT082CV


title: BNab_ADT06JT1


title: CY88_3_B04_S592_comb


title: cy79_p4_CD45_neg_PDL1_neg_F08_S1124_comb


title: BNab_DDT052KR

value: Male


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_D10_S334_comb

value: Tirosh


title: Control_FDT033GN


title: CY88_5_H08_S764_comb

value: Mal


title: CY88_3_G09_S657_comb


title: BNab_CDT052KF


title: BNab_FDT052K3


title: Control_DDT0THCH


title: cy79_p5_CD45_neg_PDL1_neg_D03_S807_comb


title: BNab_FDT07ZKM


title: CY88_3_D07_S619_comb


title: cy81_FNA_CD45_neg_F08_S1028_comb


title: cy79_p5_CD45_neg_PDL1_pos_G11_S755_comb


title: Control_CDT00QZ5


title: BNab_HDT06PCB

value: South Africa


title: cy82_CD45_pos_3_B11_S23_comb


title: Control_CDT082FB

value: Female


title: BNab_HDT06PC2


title: cy79_p5_CD45_neg_PDL1_neg_E02_S818_comb


title: cy81_FNA_CD45_neg_G12_S1044_comb


title: CY89NEG_H11_S95_comb


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_D11_S335_comb


title: BNab_BDT0613Q


title: Control_GDT0826X


title: Control_JDT06HKC


title: Control_FDT0827K


title: BNab_BDT06FQY


title: BNab_EDT06FYR


title: CY88_5_E04_S724_comb


title: cy79_p3_CD45_neg_PDL1_neg_F09_S261_comb


title: BNab_BDTO6FXR


title: Control_KDT082CK


title: BNab_CDT033GS


title: Control_DDT0TGZX


title: CY88_5_H03_S759_comb


title: CY89CORE11_A04_S100_comb


title: Control_ADT0VSQM


title: Cy71_CD45_G08_S560_comb


title: Control_CDT0833D


title: Control_JDT0831P


title: cy81_Bulk_CD45_neg_D09_S141_comb


title: BNab_BDT0615B


title: cy81_Bulk_CD45_neg_C11_S131_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_H01_S181_comb


title: cy81_Bulk_CD45_neg_E04_S148_comb


title: cy78_CD45_neg_1_F06_S546_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_B08_S20_comb


title: Control_FDT06JSO


title: Control_KDT0V77L


title: Control_CDT0K1DW


title: cy81_FNA_CD45_neg_E04_S1012_comb


title: Control_CDT082NY


title: Control_JDT082TN


title: BNab_ADT06P73


title: Cy80_II_CD45_G07_S943_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_D09_S45_comb


title: Control_ADT0834L


title: cy80_CD45_neg_E02_S914_comb


title: Control_JDT0614W


title: cy80_CD45_neg_G02_S938_comb


title: BNab_GDT033GG


title: cy80_CD45_neg_D04_S904_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_F01_S157_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_A04_S4_comb


title: cy79_p4_CD45_neg_PDL1_pos_A02_S386_comb


title: Control_DDT06JZK


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_E01_S49_comb


title: Control_KDT0V3JN


title: BNab_KDT0614Y


title: BNab_ADT0614R


title: Control_GDT082BH


title: BNab_BDT06152


title: Cy81_FNA_CD45_C09_S321_comb


title: cy78_CD45_neg_3_G02_S746_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_C08_S32_comb


title: cy82_CD45_pos_2_D11_S527_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_F06_S66_comb


title: CY88_5_D11_S719_comb


title: CY89FNAQ2_F06_S450_comb


title: BNab_EDT07ZSG


title: Control_GDT08228

value: Malawi


title: BNab_GDT0736P


title: Control_DDT08GTB


title: BNab_BDT07ZNY


title: Cy71_CD45_E11_S539_comb


title: Cy81_FNA_CD45_G10_S370_comb


title: cy78_CD45_neg_1_H07_S571_comb


title: cy78_CD45_neg_2_C06_S606_comb


title: BNab_KDT0736S


title: cy79_p4_CD45_neg_PDL1_pos_G08_S464_comb


title: Control_KDT082WK


title: BNab_JDT0735X


title: BNab_HDT06FP9


title: cy78_CD45_neg_1_B02_S494_comb


title: Control_BDT081ZZ


title: BNab_KDT0735T


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_B02_S14_comb


title: BNab_GDT06P5N


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_B12_S24_comb


title: Control_ADT08290


title: BNab_JDT06P5K


title: cy78_CD45_neg_1_E07_S535_comb


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_B08_S308_comb


title: BNab_GDT06147


title: CY88_3_C10_S610_comb


title: Control_CDT0828T


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_D05_S137_comb


title: Cy80_II_CD45_D11_S911_comb


title: Cy81_Bulk_CD45_E04_S148_comb


title: CY89NEG_B03_S15_comb


title: Control_HDT0615D


title: BNab_EDT07ZLT


title: Control_JDT0615G


title: BNab_GDT052NL


title: BNab_EDTO6G1N


title: Control_BDT082QF


title: Cy80_II_CD45_B11_S887_comb


title: CY88_3_H11_S671_comb


title: BNab_DDT052NJ


title: cy80_CD45_neg_A09_S873_comb


title: CY89NEG_G01_S73_comb


title: BNab_DDT06FRH


title: Cy80_II_CD45_H09_S957_comb


title: Control_BDT08346


title: BNab_CDT052MR


title: cy80_CD45_neg_G04_S940_comb


title: Control_GDT1451Z


title: BNab_GDT06P5X


title: cy78_CD45_neg_1_E03_S531_comb


title: cy94_cd45neg_cd90pos_E08_S344_comb


title: Control_CDT0VBP1


title: Control_DDT06158


title: cy79_p4_CD45_neg_PDL1_neg_C03_S1083_comb


title: Control_BDT0824M


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_D12_S144_comb


title: cy78_CD45_neg_1_A05_S485_comb


title: BNab_GDT060M2


title: Cy71_CD45_G02_S554_comb


title: Control_EDT17D5C


title: CY88_3_F05_S641_comb


title: BNab_BDT17BWJ


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_B10_S118_comb


title: Control_KDT179LM


title: Control_BDT17K6X


title: cy79_p3_CD45_neg_PDL1_neg_H04_S280_comb


title: CY88_5_G04_S748_comb


title: Control_KDT082GG


title: cy81_FNA_CD45_neg_C09_S993_comb


title: BNab_DDT178LQ


title: CY89CORE11_B10_S118_comb


title: CY89NEG_C03_S27_comb


title: cy81_Bulk_CD45_neg_G01_S169_comb


title: Control_BDT17DSJ


title: cy78_CD45_neg_1_C02_S506_comb


title: Cy71_CD45_E12_S540_comb


title: cy79_p3_CD45_neg_PDL1_neg_A08_S200_comb


title: BOFS#3_p2hNCC

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

institute: Center for Molecular Medicine Cologne

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human  reference assembly (hg38) using TopHat2
Read count means, fold-change (FC) and p-values were calculated with DEseq2
gene expression for the individual samples was calculated with Cufflinks as FPKMs.
Genome_build: hg38
Supplementary_files_format_and_content: Txt file containing Read count means, fold-change (FC) and p-values  calculated with DEseq2 and FPKMs calculated with Cufflinks for human Ensembl Genes used in GREAT (McLean et al., 2010).

source_name: BOFS p2hNCC

growth_protocol: WT hiPSC and BOFS hiPSC lines were grown in tissue culture plates coated with GelTrex (ThermoFisher Scientific, #1413301) using either mTeSRTM1 (STEMCELL Technologies, #05870) or StemMACS iPS-Brew XF medium (Miltenyl Biotec, #130-104-368). The medium of the cells was changed daily. hiPSC were differentiated into hNCC experiments as previously reported (Bajpai et al;2010). Briefly, hiPSCs were washed twice with PBS  and treated with 2mg/mL Collagenase solution (Life Technologies, #17104-019) in DMEM KO Medium to detach hiPSC colonies from the plate surface. 2mL of Collagenase solution was used for one well of a 6-well plate, followed with incubation period at 37C. After about one hour, collagenase solution was carefully aspirated and PBS was added to collect all the colonies into a 15mL falcon tube. Following another round of PBS washing, fresh pre-warmed hNCC Differentiation Medium  was added and resuspended to break big colonies into relatively smaller cell clumps. hiPSC clumps were then plated in petri dishes and kept at 37⁰C, which  after 2-3 days form floating Embryoid Bodies (EB) formation . Between day 6 and 9, EBs attached and gave rise to hNCC outgrowths. hNCC were collected at day 11 (d11hNCC) and then expanded for two passages (p2hNCC) according to a recent protocol (Prescott et al; 2015). The hNCC differentiation medium was changed every 2-3 days.

extract_protocol:
Total RNA was isolated using Tripure reagent according to the manufacturer’s instructions (Roche). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BOFS hiPSC were derived from fibroblasts isolated from a BOFS patient carrying a 88Mb de novo heterozygousinversion in chromosome 6.

tag: cell line

value: BOFS hiPSC cl3

tag: treatment

value: hiPSC differentiation into hNCC (passage 2)

tag: genotype

value: BOFS 88Mb inversion


title: cy94_cd45neg_cd90pos_G07_S367_comb


title: Cy81_FNA_CD45_D09_S333_comb


title: cy81_Bulk_CD45_neg_C03_S123_comb


title: CY89CORE11_F05_S161_comb


title: BOFS#2_p2hNCC

value: BOFS hiPSC cl2


title: cy79_p4_CD45_neg_PDL1_neg_C12_S1092_comb


title: BOFS#1_p2hNCC

value: BOFS hiPSC cl1


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_B07_S19_comb


title: cy79_p4_CD45_neg_PDL1_neg_B08_S1076_comb


title: Cy80_II_CD45_H07_S955_comb


title: WT#2_p2hNCC

source_name: WT p2hNCC

value: WT hiPSC#2

value: WT


title: WT#1_p2hNCC

value: WT hiPSC#1


title: CY88CD45_150813_G04_S364_comb


title: Cy81_Bulk_CD45_E10_S154_comb


title: WT_p2hNCC_TFAP2A_rep1

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human (hg19) or chicken (gg4) genome reference assembly using BWA
Normalized bedGraph files were generated using DeepTools
Peaks were called using MACS2
Genome_build: hg19; gg4

growth_protocol: WT hiPSC and BOFS hiPSC lines were grown in tissue culture plates coated with GelTrex (ThermoFisher Scientific, #1413301) using either mTeSRTM1 (STEMCELL Technologies, #05870) or StemMACS iPS-Brew XF medium (Miltenyl Biotec, #130-104-368). The medium of the cells was changed daily. hiPSC were differentiated into hNCC experiments as previously reported (Bajpai et al;2010). Briefly, hiPSCs were washed twice with PBS  and treated with 2mg/mL Collagenase solution (Life Technologies, #17104-019) in DMEM KO Medium to detach hiPSC colonies from the plate surface. 2mL of Collagenase solution was used for one well of a 6-well plate, followed with incubation period at 37C. After about one hour, collagenase solution was carefully aspirated and PBS was added to collect all the colonies into a 15mL falcon tube. Following another round of PBS washing, fresh pre-warmed hNCC Differentiation Medium  was added and resuspended to break big colonies into relatively smaller cell clumps. hiPSC clumps were then plated in petri dishes and kept at 37⁰C, which  after 2-3 days form floating Embryoid Bodies (EB) formation . Between day 6 and 9, EBs attached and gave rise to hNCC outgrowths. hNCC were collected at day 11 (d11hNCC) or expanded for two passages (p2hNCC) according to a recent protocol (Prescott et al; 2015). The hNCC differentiation medium was changed every 2-3 days. Chicken frontonasal prominences (FNP) were dissected from stage HH24 chicken embryos.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case.
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

tag: chip antibody

value: TFAP2A (sc-12726, Santa Cruz)


title: cy78_CD45_neg_1_H01_S565_comb


title: cy79_p5_CD45_neg_PDL1_pos_B02_S686_comb


title: WT_p2hNCC_input


title: WT_p2hNCC_H3K27ac

value: H3K27ac (39133, Active Motif)


title: CY88_5_C12_S708_comb


title: WT_p2hNCC_H3K27me3

value: H3K27me3 (39155, Active Motif)


title: cy78_CD45_neg_1_G05_S557_comb


title: cy78_CD45_neg_3_G11_S755_comb


title: WT_p2hNCC_H3K9me3

value: H3K9me3 (39161, Active Motif)


title: BOFS_p2hNCC_TFAP2A_rep1


title: BOFS_p2hNCC_TFAP2A_rep2


title: cy78_CD45_neg_3_D10_S718_comb

value: Tirosh


title: cy79_p5_CD45_neg_PDL1_pos_D05_S713_comb

value: Mal


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_G10_S82_comb


title: BOFS_p2hNCC_H3K27me3


title: cy81_FNA_CD45_neg_F09_S1029_comb


title: BOFS_p2hNCC_H3K27ac


title: cy79_p3_CD45_neg_PDL1_neg_H12_S288_comb


title: cy82_CD45_pos_3_A03_S3_comb

value: Undetermined


title: BOFS_p2hNCC_input


title: WT_p2hNCC_TFAP2A_rep2


title: Cy81_FNA_CD45_E05_S341_comb


title: BOFS_p2hNCC_H3K9me3


title: WT_d11hNCC_ATACseq_2

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human (hg19) or chicken (gg4) genome reference assembly using BWA
Normalized bedGraph files were generated using DeepTools
Genome_build: hg19; gg4
Genome_build: WT_d11hNCC_ATACseq.bedGraph; bedGraph; WT_d11hNCC_ATACseq_1 and WT_d11hNCC_ATACseq_2 samples were merged and then mapped before generating a single bedgraph file.
Genome_build: FNP_ATACseq_gg.bedGraph

source_name: WT d11hNCC

growth_protocol: WT hiPSC and BOFS hiPSC lines were grown in tissue culture plates coated with GelTrex (ThermoFisher Scientific, #1413301) using either mTeSRTM1 (STEMCELL Technologies, #05870) or StemMACS iPS-Brew XF medium (Miltenyl Biotec, #130-104-368). The medium of the cells was changed daily. hiPSC were differentiated into hNCC experiments as previously reported (Bajpai et al;2010). Briefly, hiPSCs were washed twice with PBS  and treated with 2mg/mL Collagenase solution (Life Technologies, #17104-019) in DMEM KO Medium to detach hiPSC colonies from the plate surface. 2mL of Collagenase solution was used for one well of a 6-well plate, followed with incubation period at 37C. After about one hour, collagenase solution was carefully aspirated and PBS was added to collect all the colonies into a 15mL falcon tube. Following another round of PBS washing, fresh pre-warmed hNCC Differentiation Medium  was added and resuspended to break big colonies into relatively smaller cell clumps. hiPSC clumps were then plated in petri dishes and kept at 37⁰C, which  after 2-3 days form floating Embryoid Bodies (EB) formation . Between day 6 and 9, EBs attached and gave rise to hNCC outgrowths. hNCC were collected at day 11 (d11hNCC). The hNCC differentiation medium was changed every 2-3 days. Chicken frontonasal prominences (FNP) were dissected from stage HH24 chicken embryos.

extract_protocol:
Approximately 50000 cells were used for each ATAC-seq assay following a previously described protocol (Buenrostro et al. 2013). Briefly, isolated nuclei were resuspended in the transposase reaction mix (25 µl 2x TD buffer, 10 µl transposase (TruSight One Kit), 15 µl nuclease-free H2O) and incubate for 30 min at 37°C. After transposition, DNA was purified using Qiagen MinElute PCR purification kit according to the manufacturer’s protocol and eluted in 10 µl elution buffer. Purified DNA samples were used for library preparation and sequencing.
ATAC-Seq library was generated by Nextera sample prep kit (Illumina).

value: hiPSC differentiation into hNCC (day 11)


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_A10_S10_comb


title: cy81_FNA_CD45_neg_B01_S973_comb


title: WT_d11hNCC_ATACseq_1


title: cy78_CD45_neg_3_D04_S712_comb


title: cy79_p5_CD45_neg_PDL1_neg_C03_S795_comb


title: cy81_Bulk_CD45_neg_A10_S106_comb


title: cy53_1_CD45_neg_E04_S340_comb


title: BOFS_p2hNCC_TFAP2A_Prom

data_processing:
Library strategy: 4C-seq
Reads were assigned to samples based on the first 10 bases of the read. Subsequently, the primer sequence was removed from the read and the remaining sequence was trimmed to 36 bases. These 36 bases were aligned to the human (hg19) or chicken (gg3) reference genomes  using Bowtie 0.12.7.
The resulting mapped reads were analyzed with R3C-seq (Thongjuea et al., 2013) in order to generate RPM (reads per million) normalized bedgraph files for downstream visualization and analysis.
Genome_build: hg19; gg3

extract_protocol:
4C-seq assays were performed as previously described (Splinter et al., 2012; Stadhouders et al., 2013; Cruz-Molina et al., 2017) with slight modifications. Approximately 5-10 million hiPSC, hNCC or chicken FNP cells were crosslinked with 1% formaldehyde during 20 minutes and quenched with 0.125M glycine for 10 min. Cells were washed with PBS and resuspended in lysis buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1X protease inhibitors) during 10 min on ice.  Following centrifugation for 5 min at 650g (4 °C), nuclei were re-suspended in 0.5 ml of 1.2X restriction buffer with 0.3% SDS and incubated at 37 °C and 900 rpm for 1h. After that, Triton X-100 was added to a final concentration of 2% followed by 1h incubation at 37 °C and 900 rpm. Afterwards, chromatin was digested overnight at 37 °C and 900 rpm with 400 U of NlaIII (R0125L, NEB). NlaIII was inactivated by adding SDS to a final concentration of 1.6% and incubating the mixture for 20 min at 65 °C while shaking (900 rpm). The digested chromatin was transferred to 50-ml tubes and 6.125 ml of 1.15X ligation buffer (50 mM Tris-HCl pH 7.6, 10 mM MgCl2, 1 mM ATP, 1mM DTT) were added. Triton X-100 was also added to a final concentration of 1% and the resulting solution was incubated for 1 h at 37 °C while shaking gently. After that, digested chromatin was ligated with 100 U of T4 DNA ligase (15224-041, Life Technologies) for 8 h at 16 °C, followed by RNAse A treatment (300 μg, Peqlab) for 45 min at 37 °C. Subsequently, chromatin was de-crosslinked with 300 μg of Proteinase K (Peqlab) and overnight incubation at 65 °C. DNA was then purified by phenol/chloroform extraction followed by ethanol precipitation and re-suspension in 100 μl of water. At this step, the digestion and ligation efficiencies were evaluated by analysing a small fraction of the purified DNAs by agarose electrophoresis. The remaining DNA was digested with 50U of DpnII (R0543M, NEB) in 500 μl of 1x NEBuffer DpnII at 37 °C overnight. DNA samples were purified by phenol/chlorophorm extraction, followed by ethanol precipitation. Once purified, DNA samples were re-suspended in 500 μl of water and a second ligation was performed by adding 200 U of T4 DNA Ligase into a final volume of 14 ml 1X ligation buffer followed by overnight incubation at 16 °C. DNA samples were subjected to another round of phenol/chlorophorm extraction and ethanol precipitation, re-suspended in 100 μl of water and purified with a QIAgen PCR purification column (28104, QIAgen). The efficiencies of the second digestion and ligation were also evaluated by agarose electrophoresis.
4C samples were amplified by inverse PCR using primers located within different human (TFAP2A promoter, ENh480, Enh100) or chicken (3' TFAP2A) genomic regions and that included illumina adaptor sequences and short barcodes. The inverse PCRs were performed with the expand long template PCR system (11681842001, Roche) and 30 amplification cycles (94°C 2 min, 30x [94°C 10 sec, 60°C 1 min, 68°C 3 min], 68°C 5 min). The inverse PCR primers were designed as previously described (Stadhouders et al., 2013). Once amplified, 4C-seq libraries were sequenced on the HiSeq2500, generating reads of either 74 or 100 bp in length.


title: BOFS_p2hNCC_TFAP2A_6p24BP_inv


title: BOFS_p2hNCC_TFAP2A_6p24BP_WTallele


title: WT_d11hNCC_TFAP2A_Enh100

value: hiPSC differentiation into hNCC (day11)


title: cy79_p3_CD45_neg_PD1_pos_AS_C3_R1_C01_S313_comb


title: cy78_CD45_neg_3_B02_S686_comb


title: WT_d11hNCC_TFAP2A_Enh480


title: WT_d11hNCC_TFAP2A_prom


title: WT_hiPSC_TFAP2A_Enh100_1

source_name: WT hiPSC


title: WT_hiPSC_TFAP2A_Enh100_2


title: WT_hiPSC_TFAP2A_Enh480_1


title: CY89CORE11_A11_S107_comb


title: cy78_CD45_neg_1_E02_S530_comb


title: cy79_p5_CD45_neg_PDL1_neg_A02_S770_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_F07_S163_comb


title: cy79_p4_CD45_neg_PDL1_neg_D01_S1093_comb


title: WT_hiPSC_TFAP2A_Prom_1


title: cy78_CD45_neg_3_E02_S722_comb


title: WT_hiPSC_TFAP2A_Enh480_2


title: WT_hiPSC_TFAP2A_Prom_2


title: cy80_CD45_neg_G01_S937_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_D02_S134_comb


title: cy79_p3_CD45_neg_PDL1_neg_F04_S256_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_C01_S121_comb


title: cy78_CD45_neg_2_B08_S596_comb


title: Cy80_II_CD45_C09_S897_comb


title: cy81_FNA_CD45_neg_D04_S1000_comb


title: cy78_CD45_neg_3_D01_S709_comb


title: cy78_CD45_neg_1_D07_S523_comb


title: CY89NEG_E07_S55_comb


title: CY89CORE11_G02_S170_comb


title: CY88_3_C01_S601_comb


title: cy79_p5_CD45_neg_PDL1_pos_A04_S676_comb


title: CY88_3_F01_S637_comb


title: cy79_p5_CD45_neg_PDL1_neg_F10_S838_comb


title: Cy81_Bulk_CD45_B10_S118_comb


title: cy79_p4_CD45_neg_PDL1_neg_H11_S1151_comb


title: Cy80_II_CD45_B07_S883_comb


title: cy79_p3_CD45_neg_PDL1_neg_E04_S244_comb


title: CY88_5_B06_S690_comb


title: Cy71_CD45_D08_S524_comb


title: Cy81_FNA_CD45_B01_S301_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_C04_S28_comb


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_D06_S138_comb


title: CY88_3_D02_S614_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_G01_S73_comb


title: cy82_CD45_pos_2_H12_S576_comb

value: Macrophage


title: cy79_p1_CD45_neg_PDL1_neg_AS_C4_R1_D09_S141_comb


title: cy78_CD45_neg_3_H06_S762_comb


title: cy79_p4_CD45_neg_PDL1_neg_E11_S1115_comb


title: Cy71_CD45_B05_S497_comb


title: HSSYII_SS18-SSX1_DMSO

city: Dublin

first: Gerard

middle: L

last: Brien

address: Lincoln Place Gate

department: Genetics

country: Ireland

institute: Trinity College Dublin

description: Treated with DMSO for 24hrs.

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 with default parameters.
Duplicate reads were removed.
BAM files were converted to bed files using a custom script, and converted to BigWig using bedtobigwig.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bigwig: bigWig files containing read normalized read densities.

source_name: Synovial sarcoma cells

growth_protocol: HSSYII cells were grown in DMEM media (Gibco, cat no. 10566-016), supplemented with 10% heat-inactivated FBS (Gibco, cat no. 10082147) and 1% Penicillin/Streptomycin (Gibco, cat no. 15140122).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/protein-DNA complexes were isolated using antibodies.
Libraries were constructed using the Rubicon Genomics DNA ThruPlex library preparation kit, catalog number R400427, in accordance with the manufacturer's instructions.

treatment_protocol: Cells were grown in media as described above containing 0.0001% DMSO or dBRD9A (100nM final concentration) for 24 hours.

value: HSSYII

value: SS18-SSX1 fusion protein containing synovial sarcoma cells

tag: passages

value: DMSO 24h

value: HA-tag (CST, 3724S)


title: HSSYII_SS18-SSX1_dBRD9A

description: Treated with dBRD9-A at 100nM for 24hrs.

value: dBRD9-A 100nM 24h


title: HSSYII_RNAPII

description: Untreated, steady state.

value: Untreated

value: RNAPII (Diagenode, C15100055-100)


title: HSSYII_Input


title: HSSYII_H3K27Ac

description: Untreated, steady state.

value: H3K27Ac (Abcam, ab4729)


title: HSSYII_BRD9_dBRD9A


title: HSSYII_BRD9_DMSO_BI7273_matched

description: Treated with DMSO for 24hrs.


title: HSSYII_BRD9_BI7273

description: Treated with BI7273 at 10uM for 24hrs.


title: HSSYII_3xHA_WT

description: Expressing exogenous 3xHA tagged BRD9-WT.

value: exogenous 3xHA tagged BRD9-WT


title: cy53_1_CD45_neg_C06_S318_comb


title: cy79_p1_CD45_neg_PDL1_pos_AS_C1_R1_F07_S67_comb


title: HSSYII_3xHA_N216A

description: Expressing exogenous 3xHA tagged BRD9-N216.

value: exogenous 3xHA tagged BRD9-N216


title: HSSYII_shSS18-SSX1-1_rep2

data_processing:
Reads were aligned to human genome assembly hg19 using STAR with default parameters.
Read count tables were created using FeatureCounts using UCSC refFlat gene models.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Total mRNA was extracted from 1 million harvested cells using the Qiagen RNeasy RNA extraction kit in accordance with the manufacturer's instructions.
Libraries were generated using the NEB, NEBNext Ultra II RNA Library Prep kit for Illumina in accordance with the manufacturer's instructions.

treatment_protocol: Cells were grown in media as described above containing 0.0001% DMSO or dBRD9A (100nM final concentration) for 6 hours. For shRNA knockdown experiments, cells were infected with GFP tagged shRNA expressing lentivirus at an viral MOI of 1.0, cells were subsequently cultured without drug selection for a total of 96hrs post-infection.


title: HSSYII_shRenilla_rep3

value: shRenilla


title: HSSYII_shRenilla_rep2


title: HSSYII_shSS18-SSX1-2_rep1


title: HSSYII_shSS18-SSX1-2_rep2


title: HSSYII_shSS18-SSX1-1_rep3


title: HSSYII_shSS18-SSX1-1_rep1


title: cy78_CD45_neg_1_B04_S496_comb

value: Tirosh


title: HSSYII_DMSO_rep2

value: DMSO 6h


title: HSSYII_shRenilla_rep1


title: HSSYII_dBRD9A_6h_rep3

value: dBRD9A 6h


title: HSSYII_dBRD9A_6h_rep2


title: HSSYII_DMSO_rep3


title: HSSYII_DMSO_rep1


title: RNA-seq JURKAT JQ1 inhibitor Rep 3

city: Chicago

first: Panagiotis

last: Ntziachristos

state: IL

address: 320 E Superior

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed for inhibitor versus control. Analysis was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values. Bigwig of RNA-seq tracks in positive and minus strands.

source_name: JURKAT

growth_protocol: cells in suspension, growing in RPMI

extract_protocol:
RNeasy kit (Qiagen)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 50bp single-read method.

treatment_protocol: cells treated with the GSI inhibitor against the NOTCH1 pathway, and JQ1inhibitor against the BRD4 histone acetylase. In addition there was a DMSO control.

value: JURKAT

value: human T cell leukemia cells

value: GSI inhibitor


title: RNA-seq JURKAT JQ1 inhibitor Rep 1


title: RNA-seq JURKAT JQ1 inhibitor Rep 2


title: HSSYII_3xHA_vector

description: Expressing 3xHA empty vector.

value: HSSYII

value: 3xHA empty vector


title: RNA-seq JURKAT GSI inhibitor Rep 2


title: HSSYII_shSS18-SSX1-2_rep3

value: SS18-SSX1 fusion protein containing synovial sarcoma cells


title: RNA-seq JURKAT GSI inhibitor Rep 1


title: RNA-seq JURKAT GSI inhibitor Rep 3


title: RNA-seq JURKAT DMSO Rep 3

value: DMSO


title: RNA-seq JURKAT DMSO Rep 2


title: RNA-seq JURKAT DMSO Rep 1


title: RNA-seq JURKAT shUSP7 technical replicate 3 biological replicate 2

treatment_protocol: cells treated with shUSP7 or PLKO empty vector.

tag: vector


title: RNA-seq JURKAT shUSP7 technical replicate 2 biological replicate 2


title: HSSYII_dBRD9A_6h_rep1


title: RNA-seq JURKAT PLKO technical replicate 1 biological replicate 1

value: PLKO


title: RNA-seq JURKAT PLKO technical replicate 1 biological replicate 2


title: RNA-seq JURKAT PLKO technical replicate 2 biological replicate 1


title: RNA-seq JURKAT shUSP7 technical replicate 2 biological replicate 1


title: RNA-seq JURKAT PLKO technical replicate 2 biological replicate 2


title: RNA-seq JURKAT shUSP7 technical replicate 3 biological replicate 1


title: RNA-seq JURKAT PLKO technical replicate 3 biological replicate 1


title: RNA-seq JURKAT PLKO technical replicate 3 biological replicate 2


title: ChIP-seq analysis of USP7 in untreated CUTLL1 cells replicate 1

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.1.2
MACS2 version 2.1.0 was used for ChIP-sequencing peak discovery. bedtools 2.17.0 was used for performing genomic interval mathematical operations, genomic interval annotation was done using R, ChIP-seq heatmap generation and ChIP-seq profile construction was done using ngsplot.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format containg rpm tracks and relative fold enrichments (FE)

extract_protocol:
USP7 ChIP: 10 million cells were used for the ChIP and precipitated using antibody against human USP7 (Bethyl, A300-033A).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: untreated JURKAT/CUTLL1 T leukemia cells

value: untreated

value: anti-USP7 (Bethyl, catalog# A300-033A, lot# Lot A300-033A-7)


title: Sequencing analysis of input in untreated CUTLL1 cell


title: RNA-seq JURKAT shUSP7 technical replicate 1 biological replicate 1


title: CY88_5_B10_S694_comb

value: Mal


title: Sequencing analysis of input in Jurkat cells treated with DMSO replicate 2

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.1.2
MACS2 version 2.1.0 was used for ChIP-sequencing peak discovery. bedtools 2.17.0 was used for performing genomic interval mathematical operations, genomic interval annotation was done using R, ChIP-seq heatmap generation and ChIP-seq profile construction was done using ngsplot.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format containg rpm tracks, relative fold enrichments (FE), and ChIP-seq signal minus input (subt)
Supplementary_files_format_and_content: Jurkat DMSO H3K27Ac Fold-enrichment: Fold enrichment analysis using the combined data set of Jurkat DMSO H3K27Ac rep1 and rep2
Supplementary_files_format_and_content: Jurkat USP7i9 H3K27Ac Fold-enrichment: Fold enrichment analysis using the combined data set of Jurkat USP7i H3K27Ac rep1 and rep2
Supplementary_files_format_and_content: Jurkat DMSO H3K27Ac ChIP-seq minus input: ChIP-seq signal minus input using the combined data set of Jurkat DMSO H3K27Ac rep1 and rep2
Supplementary_files_format_and_content: Jurkat USP7i H3K27Ac ChIP-seq minus input: ChIP-seq signal minus input using the combined data set of Jurkat USP7i H3K27Ac rep1 and rep2

extract_protocol:
H3K27Ac ChIP: 10 million cells were used for the ChIP and precipitated using antibody against human H3K27Ac (Cell Signaling Technology, 8173S, lot #1).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: JURKAT T leukemia cells treated with DMSO or USP7 inhibitor

tag: antibody


title: RNA-seq JURKAT DMSO replicate 2

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed for inhibitor versus control. Analysis was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values; JURKAT_DMSO_vs_USP7i9.htseq.edgeR.txt. Bigwig of RNA-seq tracks in positive and minus strands.

treatment_protocol: cells treated with USP7 inhibitor, GSI inhibitor against the NOTCH1 pathway, and GSKJ4 inhibitor against JMJD3 histone demethylase. In addition there was a DMSO control.

tag: agent


title: ChIP-seq analysis of H3K27Ac in Jurkat cells treated with USP7 inhibitor 9 replicate 1

value: H3K27Ac antibody


title: ChIP-seq analysis of H3K27Ac in Jurkat cells treated with DMSO replicate 2


title: Sequencing analysis of input in Jurkat cells treated with DMSO replicate 1


title: ChIP-seq analysis of H3K27Ac in Jurkat cells treated with USP7 inhibitor 9 replicate 2


title: RNA-seq JURKAT DMSO replicate 1


title: ChIP-seq analysis of H3K27Ac in Jurkat cells treated with DMSO replicate 1


title: RNA-seq JURKAT shUSP7 technical replicate 1 biological replicate 2


title: Sequencing analysis of input in Jurkat cells treated with USP7i9 replicate 2


title: ChIP-seq analysis of USP7 in untreated CUTLL1 cells replicate 2


title: Sequencing analysis of input in Jurkat cells treated with USP7i9 replicate 1


title: wild-type 37C MNase-seq 1

city: Boston

first: Fred

last: Winston

address: 77 Avenue Louis Pasteur, Room 239

institute: Harvard Medical School

description: MNase-seq in a wild-type S. cerevisiae strain grown at 30ºC and shifted to 37ºC for 80 minutes.

data_processing:
The Snakemake pipeline used to process MNase-seq libraries is available at github.com/winston-lab. The barcode is the first 6 bases of the read and is ACTTGA for this library . Paired-end reads were demultiplexed using fastq-multx, allowing one mismatch to the barcode. Read 2 barcode removal and 3’ quality trimming were performed with cutadapt. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie1, and correctly paired reads were selected using SAMtools. Coverage of nucleosome protection and nucleosome dyads were extracted using bedtools and custom shell scripts to get the entire fragment or the midpoint of the fragment, respectively. Smoothed nucleosome dyad coverage was generated by smoothing dyad coverage with a Gaussian kernel of 20 bp bandwidth. Coverage was normalized to the total number of correctly paired S. pombe fragments.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: TSS-seq “plus” and “minus” files are bigWig files of spike-in normalized S. cerevisiae transcription start sites on the positive and negative strands, respectively. ChIP-nexus “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the points of crosslinking on the positive and negative strand, respectively. ChIP-nexus “midpoint” and “protection” files are library-size normalized S. cerevisiae coverage of either the midpoint of the fragment predicted to be protected by the ChIP’ed factor by MACS2, or the entire fragment. NET-seq “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the positions of transcribing RNA polymerase II on the positive and negative strands, respectively. MNase-seq “midpoint” files are bigWig files of spike-in normalized S. cerevisiae dyad coverage determined by taking the midpoint of each sequenced fragment. MNase-seq “midpoint_smoothed” files are bigWig files of the same spike-in normalized dyad coverage, smoothed with a Gaussian kernel of 20bp bandwidth. MNase-seq “wholefrag” files are bigWig files of spike-in normalized S. cerevisiae  coverage of the entire fragment protected from MNase digestion.

organism: Saccharomyces cerevisiae

source_name: log phase S. cerevisiae

growth_protocol: Cells were grown in YPD at 30ºC to approximately 1x107 cells/ml (OD600=0.5), at which point an equal volume of YPD medium pre-warmed to 44ºC was added, and the cultures were shifted to 37ºC for an additional 80 minutes.

extract_protocol:
Cells were crosslinked using 2% formaldehyde for 30 minutes, then treated for 10 minutes before 125mM glycine before collecting an equal number of cells for each strain. The cells were resuspended in 40 mL of sorbitol buffer (1M sorbitol, 50mM Tris pH 7.4, 10mM β-mercaptoethanol) and incubated for 30 minutes at 30ºC with 10 mg of zymolyase 100T (US Biological) per gram of cells. Spheroplasting efficiency was assessed by microscopy and was greater than 95% of total cells. The spheroplasts were collected and resuspended in NP buffer (1M sorbitol, 50mM sodium chloride, 10mM Tris pH 7.4, 5mM magnesium chloride, 1mM calcium chloride, 0.075% NP-40, 1mM β-mercaptoethanol, 500 μM spermidine). Micrococcal nuclease (MNase) (Sigma) was dissolved in Ex50 (10mM Hepes pH 7.6, 50 mM sodium chloride, 1.5 mM magnesium chloride, 0.5 mM EGTA, 10% glycerol, 1 mM dithiothreitol, 0.2 mM phenylmethylsulfonyl fluoride) prepared to produce 500 units per 840μL stock as recommended by the manufacturer. The spheroplasts were divided into aliquots and incubated for 20 minutes at 37ºC with increasing amounts of MNase, ranging from 2 to 15 μL of the stock. Digestion was stopped by addition of stop buffer (5% SDS, 100 mM EDTA), samples were subjected to proteinase K digestion and reverse-crosslinking at 65ºC overnight, followed by DNA purification. The efficiency of MNase digestion was quantified using an Agilent Bioanalyzer to establish an MNase titration curve for each strain. The MNase concentrations yielding approximately 80% mononucleosomal DNA were selected for library construction. The samples were mixed with the MNase-digested spike-in DNA from S. pombe based on original cell count (100 ng of spike-in per MNase-digested DNA from 7x108 S. cerevisiae cells). Mononucleosomal DNA was purified by size-selected gel extraction.
Libraries were constructed as previously described (DeGennaro, 2013)

tag: strain

tag: temperature

tag: tissue

value: log phase S. cerevisiae

tag: experiment type

value: MNase-seq

tag: target molecule

value: genomic DNA


title: spt6-1004 37C MNase-seq 1

description: MNase-seq in the spt6-1004  S. cerevisiae strain grown at 30ºC and shifted to 37ºC for 80 minutes.

data_processing:
The Snakemake pipeline used to process MNase-seq libraries is available at github.com/winston-lab. The barcode is the first 6 bases of the read and is CTTGTA for this library. Paired-end reads were demultiplexed using fastq-multx, allowing one mismatch to the barcode. Read 2 barcode removal and 3’ quality trimming were performed with cutadapt. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie1, and correctly paired reads were selected using SAMtools. Coverage of nucleosome protection and nucleosome dyads were extracted using bedtools and custom shell scripts to get the entire fragment or the midpoint of the fragment, respectively. Smoothed nucleosome dyad coverage was generated by smoothing dyad coverage with a Gaussian kernel of 20 bp bandwidth. Coverage was normalized to the total number of correctly paired S. pombe fragments.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: TSS-seq “plus” and “minus” files are bigWig files of spike-in normalized S. cerevisiae transcription start sites on the positive and negative strands, respectively. ChIP-nexus “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the points of crosslinking on the positive and negative strand, respectively. ChIP-nexus “midpoint” and “protection” files are library-size normalized S. cerevisiae coverage of either the midpoint of the fragment predicted to be protected by the ChIP’ed factor by MACS2, or the entire fragment. NET-seq “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the positions of transcribing RNA polymerase II on the positive and negative strands, respectively. MNase-seq “midpoint” files are bigWig files of spike-in normalized S. cerevisiae dyad coverage determined by taking the midpoint of each sequenced fragment. MNase-seq “midpoint_smoothed” files are bigWig files of the same spike-in normalized dyad coverage, smoothed with a Gaussian kernel of 20bp bandwidth. MNase-seq “wholefrag” files are bigWig files of spike-in normalized S. cerevisiae  coverage of the entire fragment protected from MNase digestion.


title: RNA-seq JURKAT USP7 inhibitor 9 24h replicate 2

tag: cell type

value: USP7 inhibitor 9


title: spt6-1004 37C MNase-seq 2

data_processing:
The Snakemake pipeline used to process MNase-seq libraries is available at github.com/winston-lab. The barcode is the first 8 bases of the read and is ATATAGGA for this library. Paired-end reads were demultiplexed using fastq-multx, allowing one mismatch to the barcode. Read 2 barcode removal and 3’ quality trimming were performed with cutadapt. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie1, and correctly paired reads were selected using SAMtools. Coverage of nucleosome protection and nucleosome dyads were extracted using bedtools and custom shell scripts to get the entire fragment or the midpoint of the fragment, respectively. Smoothed nucleosome dyad coverage was generated by smoothing dyad coverage with a Gaussian kernel of 20 bp bandwidth. Coverage was normalized to the total number of correctly paired S. pombe fragments.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: TSS-seq “plus” and “minus” files are bigWig files of spike-in normalized S. cerevisiae transcription start sites on the positive and negative strands, respectively. ChIP-nexus “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the points of crosslinking on the positive and negative strand, respectively. ChIP-nexus “midpoint” and “protection” files are library-size normalized S. cerevisiae coverage of either the midpoint of the fragment predicted to be protected by the ChIP’ed factor by MACS2, or the entire fragment. NET-seq “plus” and “minus” files are bigWig files of library-size normalized S. cerevisiae coverage of the positions of transcribing RNA polymerase II on the positive and negative strands, respectively. MNase-seq “midpoint” files are bigWig files of spike-in normalized S. cerevisiae dyad coverage determined by taking the midpoint of each sequenced fragment. MNase-seq “midpoint_smoothed” files are bigWig files of the same spike-in normalized dyad coverage, smoothed with a Gaussian kernel of 20bp bandwidth. MNase-seq “wholefrag” files are bigWig files of spike-in normalized S. cerevisiae  coverage of the entire fragment protected from MNase digestion.


title: Sequencing analysis of input in Jurkat cells treated with USP7i9 (control for H3K27me3 ChIP and H2AUb ChIP)

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.1.2
MACS2 version 2.1.0 was used for ChIP-sequencing peak discovery. bedtools 2.17.0 was used for performing genomic interval mathematical operations, genomic interval annotation was done using R, ChIP-seq heatmap generation and ChIP-seq profile construction was done using ngsplot.
Genome build: hg19
Supplementary_files_format_and_content: bigwig format containg rpm tracks and relative fold enrichments (FE)

source_name: Jurkat USP7i9 input

extract_protocol:
H2AUb ChIP: 10 million cells were used for the ChIP and precipitated using antibody against human H2AUb (Cell Signaling Technology, 8240S).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.


title: Sequencing analysis of input in Jurkat cells treated with DMSO (control for H2BUb ChIP)

source_name: Jurkat DMSO input

extract_protocol:
H2BUb ChIP: 10 million cells were used for the ChIP and precipitated using antibody against human H2BUb (Cell Signaling Technology, 5546S).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.


title: Sequencing analysis of input in Jurkat cells treated with USP7i9 (control for H2BUb ChIP)


title: RNA-seq USP7 inhibitor 9 21h replicate 2

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed for inhibitor versus control. Analysis was performed using edgeR.
Genome build: hg19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values. Bigwig of RNA-seq tracks in positive and minus strands.

treatment_protocol: cells infected with the USP7 inhibitor, GSI inhibitor against the NOTCH1 pathway, and GSKJ4 inhibitor against JMJD3 histone demethylase. In addition there was a DMSO control.


title: RNA-seq CUTLL1 DMSO replicate 2


title: RNA-seq USP7 inhibitor 9 21h replicate 1


title: RNA-seq GSI 21h replicate 2

value: GSI


title: RNA-seq GSI 21h replicate 1


title: RNA-seq GSKJ4 21h replicate 1


title: RNA-seq JURKAT USP7 inhibitor 9 24h replicate 1

value: JURKAT


title: RNA-seq GSKJ4 21h replicate 2

value: human T cell leukemia cells


title: RNA-seq CUTLL1 DMSO replicate 1


title: Sequencing analysis of input in Jurkat cells treated with USP7i9 replicate 2 (control for H3K79me2 ChIP)

extract_protocol:
H3K79me2 ChIP: 10 million cells were used for the ChIP and precipitated using antibody against human H3K79me2 (homemade, Ali Shilatifard lab).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.


title: Sequencing analysis of input in Jurkat cells treated with DMSO (control for H3K27me3 ChIP and H2AUb ChIP)


title: Sequencing analysis of input in Jurkat cells treated with USP7i9 replicate 1 (control for H3K79me2 ChIP)


title: Sequencing analysis of input in Jurkat cells treated with DMSO replicate 2 (control for H3K79me2 ChIP)


title: LNCaP shFOXA1 1#

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of FPKM values for each Sample ...

source_name: ATCC

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol:
Total RNA was isolated from cells using PureLinkTM RNA Mini Kit (Life Tech).  The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: LNCaP cells were treated with shCtr and shFOXA1 lentivirus and selected with puromycin 48h post infection.

value: LNCaP

value: prostate

tag: treatment/infection

value: WT


title: LNCaP shFOXA1 2#


title: LNCaP shFOXA1 3#


title: Sequencing analysis of input in untreated Jurkat cell (control for USP7 ChIP)

source_name: Jurkat Input

treatment_protocol: untreated JURKAT T leukemia cells


title: Sequencing analysis of input in Jurkat cells treated with DMSO replicate 1 (control for H3K79me2 ChIP)


title: ChIP-seq analysis of H2BUb in Jurkat cells treated with USP7 inhibitor 9 replicate 2

source_name: Jurkat USP7i9 H2BUb

value: anti-H2BUb (Cell Signaling Technology, catalog# 5546S, lot# 4)


title: LNCaP pGIPZ 2#

value: pGIPZ


title: LNCaP pGIPZ 3#


title: ChIP-seq analysis of H2BUb in Jurkat cells treated with USP7 inhibitor 9 replicate 1


title: ChIP-seq analysis of H2BUb in Jurkat cells treated with DMSO replicate 2

source_name: Jurkat DMSO H2BUb

value: DMSO


title: LNCaP pGIPZ 1#


title: ChIP-seq analysis of H2AUb in Jurkat cells treated with USP7 inhibitor 9 replicate 2

source_name: Jurkat USP7i9 H2AUb

value: anti-H2AUb (Cell Signaling Technology, catalog# 8240S, lot# 2)


title: SM3

city: Geneva

first: Thilo

last: Kohler

address: 1, rue Michel Servet

department: Microbiology and Molecular Medicine

institute: University of Geneva

data_processing:
The reads were mapped with the TopHat v.2 software to the Pseudomonas aeruginosa PA14 RefSeq genome NC_008463.1 for the PM samples, the Staphylococcus aureus Newman RefSeq genome NC_009641.1 for the SM samples and a merge of the two for the CC samples
The table of counts with the number of reads mapping to each gene feature of to the Pseudomonas aeruginosa PA14 RefSeq genome NC_008463.1 for the PM samples, the Staphylococcus aureus Newman RefSeq genome NC_009641.1 for the SM samples and a merge of the two for the CC samples was prepared with HTSeq v0.5.3p9
The differential expression analysis was performed with the statistical analysis R/Bioconductor package EdgeR v. 3.4.2.
The genes having a count above 1 count per million reads (cpm) in at least 3 samples were kept for the analysis. The differentially expressed genes tests were done with the exactTest() function using the exact negative binomial test.
Genome_build: PA14 RefSeq genome NC_008463.1 for the PM samples, the Staphylococcus aureus Newman RefSeq genome NC_009641.1 for the SM samples and a merge of the two for the CC samples
Supplementary_files_format_and_content: CPM

organism: Staphylococcus aureus

source_name: S. aureus monoculture replicate 3

growth_protocol: M14 medium

extract_protocol:
RNA was extracted after 3 h of co-culture
RNA were ribodepleted with the Ribo-Zero rRNA Removal kit (Bacteria) from Illumina (formely Epicentre) with 1300 ng as input material. Libraries were prepared with the Illumina TruSeq Stranded Total RNA kit according to manufacturer's specifications.
Ribo-depleted RNA-seq

treatment_protocol: RNA stabilized in Bacteria Protect reagent (Qiagen)

tag: strains

value: Newman

value: 3h monoculture in M14 medium


title: ChIP-seq analysis of H2AUb in Jurkat cells treated with DMSO replicate 2

source_name: Jurkat DMSO H2AUb


title: ChIP-seq analysis of H2BUb in Jurkat cells treated with DMSO replicate 1


title: ChIP-seq analysis of H2AUb in Jurkat cells treated with DMSO replicate 1


title: ChIP-seq analysis of H2AUb in Jurkat cells treated with USP7 inhibitor 9 replicate 1


title: SM2

source_name: S. aureus monoculture replicate 2


title: 387_H3K27me3_ChIPseq

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

description: H3K27me3 ChIP-seq from patient derived glioblastoma cell specimens

data_processing:
FASTQ files were trimmed with Trim Galore and aligned to the hg19 genome using BWA (for ChIPseq) or Bowtie2 (for N6mA DIPseq) as described in the methods.
SAM files were sorted and duplicates were removed using PicardTools as described in the methods
Bigwigs were generated from BAM files using DeepTools
Peaks were called using the EPIC implementation of the SICER algorithm as described in the methods. For differential peak calling, the Non-targeting shRNA file was used as the input, as described in the methods.
See methods section in manuscript for complete data processing details for ChIP, DIP, and Bisulfite sequencing analysis
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG and BED files

source_name: Patient Derived Glioblastoma Stem Cell

growth_protocol:
Cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.
Cells were grown in neurobasal media supplemented with sodium pyruvate, B27, glutamax, EGF/FGF, and penicillin/streptomycin as described in more detail in the methods. Cells were treated with the indicated shRNA.

extract_protocol:
DNA extraction protocol is described in the method section
For ChIP-seq and N6-mA DIPseq, NEB NEBNext® Ultra™ DNA Library Prep Kit

treatment_protocol:
For N6mA DIPseq, Rabbit polyclonal antibody to N6-mA (Synaptic Systems, Cat#202-003) was used.
For H3K9me3 ChIPseq, rabbit polyclonal antibody to Histone H3K9me3 (Abcam,Cat#ab8898) was used
For H3K27me3 ChIPseq, rabbit polyclonal antibody to Histone H3K27me3 , (Active Motif, Cat#39155) was used
For H3K4me3 ChIPseq, rabbit polyclonal antibody to Histone H3K4me3 (Abcam,Cat#8580)
For ALKBH1 ChIPseq, rabit polyclonal antibody to ALKBH1 (Abcam, Cat#ab126596) was used
Chromatin Immunoprecipitation (ChIP) was performed as previously described. Briefly, formaldehyde-fixed cells were lysed and sheared (Branson S220) on wet ice. The sheared chromatin was cleared and incubated overnight at 4  C with 5  mg H3K9me3 antibody (Abcam, ab8898), H3K27me3 (active motif, 39155), or H3K4me3 (Abcam) respectively. Antibody-chromatin complexes were immunoprecipitated with protein G magnetic Dynal beads (Life Technologies), washed, eluted, reverse crosslinked, and treated with RNAse A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Beckmann Coulter) and then used to prepare sequencing libraries by NEB NEBNext   Ultra    DNA Library Prep Kit for Illumina for sequencing.
For N6mA DIPsequencing, briefly, genomic DNA from patient-derived glioblastoma stem cell models was purified with a DNeasy kit (QIAGEN, 69504). For each sample, 5   g DNA was sonicated to 200   300 bp with Bioruptor. Then, adaptors were ligated to genomic DNA fragments following the Illumina protocol. The ligated DNA fragments were denatured at 95 degree for 5 minutes. Then, the single-stranded DNA fragments were immunoprecipitated with N6-mA antibodies (5   g for each reaction, 202-003, Synaptic Systems) overnight at 4  C. N6-mA enriched DNA fragments were purified according to the Active Motif hMeDIP protocol. IP DNA and input DNA were PCR amplified with NEBNext indexing primers, and were then subjected to multiplexed library construction and sequencing with Illumina HiSeq sequencing

tag: cell treatment

value: No Treatment


title: 387_ALKBH1_CHIP

description: ALKBH1 ChIP-seq from patient derived glioblastoma cell specimens


title: 387_H3K4me3_ChIPseq

description: H3K4me3 ChIP-seq from patient derived glioblastoma cell specimens

value: No treatment


title: 387_Input for ALKBH1 ChIP

description: Input ChIP-seq from patient derived glioblastoma stem cell specimens


title: 387_H3K9me3_ChIPseq

description: H3K9me3 ChIP-seq from patient derived glioblastoma cell specimens


title: SM1

source_name: S. aureus monoculture replicate 1


title: ChIP-seq analysis of H3K27me3 in Jurkat cells treated with USP7 inhibitor 9 replicate 2

source_name: Jurkat USP7i9 H3K27me3

extract_protocol:
H3K27me3 ChIP: 10 million cells were used for the ChIP and precipitated using antibody against human H3K27me3 (Cell Signaling Technology, 9733S).
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

tag: cell line

value: anti-H3K27me3 (Cell Signaling Technology, catalog# 9733S, lot# 8)


title: ChIP-seq analysis of H3K27me3 in Jurkat cells treated with USP7 inhibitor 9 replicate 1

tag: treatment


title: 387_Input_for_HistoneModification_ChIP


title: ChIP-seq analysis of H3K27me3 in Jurkat cells treated with DMSO replicate 1

source_name: Jurkat DMSO H3K27me3


title: T387_shALKBH1.1551_H3K9me3_ChIPseq

description: H3K9me3 ChIP-seq from patient derived glioblastoma stem cell specimens

value: Cells were treated with an shRNA targeting ALKBH1 (shALKBH1.1551)


title: T387_shCONT_H3K9me3_ChIPseq

value: Cells were treated with a non-targeting shRNA (shCONT)


title: ChIP-seq analysis of H3K27me3 in Jurkat cells treated with DMSO replicate 2


title: ChIP-seq analysis of H3K79me2 in Jurkat cells treated with USP7 inhibitor 9 replicate 2

source_name: Jurkat USP7i9 H3K79me2

value: H3K79me2 (homemade, Ali Shilatifard lab)


title: T387_InputforH3K9me3_ChIPseq


title: ChIP-seq analysis of H3K79me2 in Jurkat cells treated with USP7 inhibitor 9 replicate 1

value: JURKAT


title: T387_Bisulfite_Sequencing

description: Whole Genome Bisulfite Sequencing, as described in the methods


title: GSC23_Input_forH3K9me3_ChIP


title: GSC23_shALKBH1_1551_H3K9me3_ChIPseq_Rep2


title: D456_Input_forH3K9me3_ChIP


title: ChIP-seq analysis of H3K79me2 in Jurkat cells treated with DMSO replicate 2

source_name: Jurkat DMSO H3K79me2

value: human T cell leukemia cells


title: ChIP-seq analysis of H3K79me2 in Jurkat cells treated with DMSO replicate 1


title: GSC23_shCONT_H3K9me3_ChIPseq_Rep2

value: Cells were treated with an shRNA targeting ALKBH1


title: ChIP-seq analysis of USP7 in untreated Jurkat cells replicate 2

source_name: Jurkat USP7

value: untreated

value: anti-USP7 (Bethyl, catalog# A300-033A, lot# Lot A300-033A-7)


title: T8.3mo.F.TI.4

first: Juhyun

last: Oh

address: 185 Cambridge Street

institute: Massachusetts General Hospital

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.3
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM12)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

organism: Mus musculus

source_name: Tumor

growth_protocol: 3 month old or 12 month old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC38 tumors were implanted subcutaneously and harvested for immune cell isolation at day 10 of tumor growth

tag: age

value: 3 month old

tag: sorting markers

value: CD8+ T cells


title: GSC23_shALKBH1_1551_H3K9me3_ChIPseq_Rep1


title: GSC23_shCONT_H3K9me3_ChIPseq_Rep1


title: T8.3mo.F.TI.3


title: ChIP-seq analysis of USP7 in untreated Jurkat cells replicate 1

tag: chip antibody


title: Sound wave treated tomato fruit Tomato-1KHZ_7D_03

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data for Solanum lycopersicum (tomato) were obtained from the National Center for Biotechnology Information (NCBI) genome database (assembly ID: SL2.50).
STAR was applied to tissue samples for mapping and to quantify reads to the reference genome (ver. 2.5).To estimate gene expression levels, counts per million (CPM) mapped reads values were calculated for each sample. The CPM data were normalised using quantile normalisation in the R language environment (version 3.2.5).
Genome_build: SL2.50
Supplementary_files_format_and_content: tab-delimited text format with log2 transformed CPM values of genes

organism: Solanum lycopersicum

source_name: Sound wave treated tomato fruit

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
The sequencing library was prepared using a TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocol. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. After the ligation of adapters, the fragments were amplified by PCR.

value: Sound wave

tag: sound frequency

value: 1 KHZ


title: Control tomato fruit Tomato-CTRL_7D_03

source_name: tomato fruit


title: Control tomato fruit Tomato-CTRL_5D_03


title: Control tomato fruit Tomato-CTRL_2D_03


title: T8.3mo.F.TI.2


title: T8.3mo.F.TI.1


title: Sound wave treated tomato fruit Tomato-1KHZ_6H_03


title: T8.3mo.F.Sp.4

source_name: Spleen


title: D456_shALKBH1_1551_H3K9me3_ChIPseq_Rep1

tag: antibody


title: D456_shCONT_H3K9me3_ChIPseq_Rep1


title: D456_shCONT_H3K9me3_ChIPseq_Rep2


title: Sound wave treated tomato fruit Tomato-1KHZ_2D_03


title: Control tomato fruit Tomato-CTRL_6H_03


title: T8.3mo.F.Sp.3


title: T8.3mo.F.Sp.2


title: T8.3mo.F.Sp.1


title: D456_shALKBH1_1551_H3K9me3_ChIPseq_Rep2


title: Sound wave treated tomato fruit Tomato-1KHZ_5D_03


title: sh-ALKBH1-4-1-ATAC

description: ATAC-seq was performed on isolated cell nuclei.

data_processing:
Adapter-trimmed fastq files were aligned to hg19 by Bowtie2 (Langmead and Salzberg, 2012) using parameters “-X2000 --mm --local“. After filtering by using samtools (Li et al., 2009) with “-q 30 -F 1804 -f 2”, only primary and proper mated reads were left to remove PCR duplicate by using “markduplicate” from Picard tools (http://broadinstitute.github.io/picard/). The remaining mapped reads were shift +4 bp and -5 bp for “+” and “-” strand respectively to adjust for TN5 dimer so that the first base of each reads represents the cutting site. Then the peak calling was performed by using MACS2 (Zhang et al., 2008) with “-f bed -p 0.01 --shift - 75 -extsize 150”. The output “narrowPeaks” were further filtered out the blacklist regions (Consortium, 2012). The detailed pipeline can be found in https://github.com/epigen-UCSD/atac_seq_pipeline , which is based on Kundaje lab’s pipeline https://github.com/kundajelab/atac_dnase_pipelines with a few small changes documented on the repo.
To calculate gained and lost peaks following ALKBH1 knockdown, ATAC-seq BAM files along with narrowpeak files were analyzed using DiffBind (https://bioconductor.org/packages/release/bioc/html/DiffBind.html) (Ross-Innes et al., 2012) and DESeq2 (Love et al., 2014) to identify regions of quantitatively differential chromatin accessibility following ALKBH1 knockdown. DiffBind was used to generate MA-plots and supervised counts heatmaps. For the generation of heatmaps and profile plots, the DeepTools “computeMatrix” , “plotHeatmap” , and “plotProfile” functions were used with specific parameters given in the figure legends of the manuscript.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bigwig and NarrowPeak Files

source_name: Patient-Derived Glioblastoma Stem Cell

growth_protocol: 387 cells from a primary patient derived GBM tumor model were injected intracranially into an immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.

extract_protocol:
ATAC-seq was performed on 50,000 nuclei. The samples were permeabilized in cold permeabilization buffer (0.2% IGEPAL-CA630 (I8896, Sigma), 1 mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)) for 10 minutes on the rotator in the cold room and centrifuged for 5 min at 500 xg at 4°C. The pellet was resuspended in cold tagmentation buffer (33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg- acetate (M2545, Sigma), 16% DMF (DX1730, EMD Millipore) in Molecular biology water (46000-CM, Corning)) and incubated with Tagmentation enzyme (FC-121-1030; Illumina) at 37 °C for 30 min with shaking 500 rpm. The tagementated DNA was purified using MinElute PCR purification kit (28004, Qiagen).
The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 minutes, denaturation at 98°C for 30s, followed by 8 cycles of denaturation at 98°C for 10 s, annealing at 63°C for 30 seconds and extension at 72°C for 60 seconds. After the purification of amplified libraries using MinElute PCR purification kit (28004, Qiagen), the double size selection was performed using SPRIselect bead (B23317, Beckman Coulter) with 0.55X beads and 1.5X to sample volume.

treatment_protocol: Cells were treated with a non-targeting shRNA (shCONT) or shRNAs targeting ALKBH1.

value: glioblastoma stem cells

tag: shRNA

value: shRNA targeting ALKBH1 (shALKBH1.1008)


title: T8.12mo.F.TI.4

tag: strain

value: 12 month old


title: HSSYII_BRD9_DMSO_dBRD9A_matched

description: Treated with DMSO for 24hrs.

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 with default parameters.
Duplicate reads were removed.
BAM files were converted to bed files using a custom script, and converted to BigWig using bedtobigwig.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bigwig: bigWig files containing read normalized read densities.

source_name: Synovial sarcoma cells

value: HSSYII

value: SS18-SSX1 fusion protein containing synovial sarcoma cells

tag: passages

value: DMSO 24h

value: HA-tag (CST, 3724S)


title: sh-ALKBH1-6-1-ATAC

value: shRNA targeting ALKBH1 (shALKBH1.1551)


title: sh-ALKBH1-6-2-ATAC


title: sh-ALKBH1-4-2-ATAC


title: T8.12mo.F.TI.3


title: NT-2-ATAC

value: non-targeting shRNA (shCONT)


title: T8.12mo.F.TI.2


title: NT-1-ATAC


title: FNP_ATACseq_gg

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human (hg19) or chicken (gg4) genome reference assembly using BWA
Normalized bedGraph files were generated using DeepTools
Genome_build: hg19; gg4
Genome_build: WT_d11hNCC_ATACseq.bedGraph; bedGraph; WT_d11hNCC_ATACseq_1 and WT_d11hNCC_ATACseq_2 samples were merged and then mapped before generating a single bedgraph file.
Genome_build: FNP_ATACseq_gg.bedGraph

organism: Gallus gallus

source_name: FNP from stage HH24 chicken embryos

extract_protocol:
Approximately 50000 cells were used for each ATAC-seq assay following a previously described protocol (Buenrostro et al. 2013). Briefly, isolated nuclei were resuspended in the transposase reaction mix (25 µl 2x TD buffer, 10 µl transposase (TruSight One Kit), 15 µl nuclease-free H2O) and incubate for 30 min at 37°C. After transposition, DNA was purified using Qiagen MinElute PCR purification kit according to the manufacturer’s protocol and eluted in 10 µl elution buffer. Purified DNA samples were used for library preparation and sequencing.
ATAC-Seq library was generated by Nextera sample prep kit (Illumina).

value: FNP

tag: genotype

value: WT


title: FNP_H3K4me2

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human (hg19) or chicken (gg4) genome reference assembly using BWA
Normalized bedGraph files were generated using DeepTools
Peaks were called using MACS2
Genome_build: hg19; gg4

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case.
DNA libraries were prepared using the Illumina TruSeq RNA sample preparation Kit v2 starting from the end repair step of the protocol. Up to 100 ng ChIP DNA was used as starting material. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified for 18 PCR cycles to create the final libraries.

value: H3K4me2 (39141, Active Motif)


title: T8.12mo.F.TI.1