title: Tbl1xKO, B3, SR2

value: mouse trophoblast stem cells (mTSCs)

value: self-renewal (SR)

value: TSGFP


title: SAM24407129, replicate 1, scRNASeq

status: Public on Apr 26 2023

type: SRA

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

country: USA

institute: Genentech

library_source: transcriptomic single cell

data_processing:
Read pseudoalignment: kallisto (version 0.46.2)
BUS file processing and gene count matrix creation: bustools (version 0.40.0)
Assembly: GRCh38 / Ensembl 90
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Lung

growth_protocol: NCI-H358 and NCI-H23 cell lines were barcoded with TraCe-seq barcoding libraries and expanded in culture to establish the starting TraCe-seq cell populations. A fraction of the starting populations were profiled by single cell RNA-sequencing (scRNA-seq) to capture the relative clonal abundance and transcriptional profile of each barcoded clones right before drug treatment. In parallel, the rest of the cells were treated with sotorasib alone or in combination with GNE-7883 until resistant clones emerged under sotorasib single agent treatment. We conducted scRNA-seq profiling to capture acute responses to the treatment at 72h post treatment as well as after resistance has emerged to capture adaptive changes. These time points were chosen to allow us capture the differential transcriptional responses in the resistant versus sensitive clones, and compare the responses to sotorasib single agent versus sotorasib + GNE-7883 combination at individual clone and single cell level.

extract_protocol:
Cultured cells were trypsinized into single cell suspensions in PBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: Carcinoma Non-Small Cell

tag: treatment

value: AMG-510 1.5um + TEADi 500nm

tag: time point

value: Day 15


title: SAM24409160, replicate 2, scRNASeq


title: 11H_M_2852

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

tag: age

tag: strain


title: SAM24407133, replicate 1, scRNASeq

value: DMSO


title: SAM24409159, replicate 3, scRNASeq

value: Baseline

value: Day 0


title: 11H_M_2851


title: 11H_M_2856


title: Tbl1xKO, B3, SR1

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic

data_processing:
read trimming: bbduk (38.86)
alignment: STAR (2.7.3a)
alignment processing: samtools (1.10)
read counting: htseq-count (0.11.2)
Genome_build: mm10
Supplementary_files_format_and_content: txt/counts

source_name: mouse trophoblast stem cells (mTSCs)

growth_protocol: Mouse TS cells were grown in a standard TS medium (RPMI 1640 supplemented with 20% fetal calf serum, 2mM L-Glutamine, 2mM sodium pyruvate and 100mM 2-mercaptoethanol) containing 70% mouse embryonic fibroblast -conditioned medium and 100 ng ml-1 Fgf2 and 1 µg ml-1 heparin. Cells were split every third day using trypsin.

extract_protocol:
Quantseq libraries were prepared with 250 ng RNA using QuantSEQ 3’ mRNA-Seq Library Prep Kit FWD for Illumina (015.96, Lexogen) according to manufacturer’s recommendations. The libraries were pooled and sequenced with a 50-base-pair single-end protocol on an Illumina HiSeq 2500 sequencer.
RNAseq. RNA was extracted using RNeasy mini kit (Qiagen) and treated with DNaseI (Qiagen).
RNA-seq (Quantseq)

treatment_protocol: For differentiation, TSCs were exposed to 3 µM PD0325901 (Tocris) in full TSC media for 24h

tag: differentiation state

tag: modification

tag: parental cell line


title: Tbl1xKO, B3, PD2

value: 24h differentiation with PD (PD)


title: A-MDL140_v1_5219

type: genomic

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Epic Human Methylation 850K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2011.1

label: Cy3, Cy5

source_name: saliva

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: male

tag: sample type

value: saliva

tag: disease state

value: normal

tag: individual

value: Control

tag: timepoint (intervention)

value: Before

value: 64 years


title: 11H_M_2850


title: Tbl1xKO, B3, PD1

value: mouse trophoblast stem cells (mTSCs)


title: A-MDL133_v2_11619

value: Midpoint

value: 57 years


title: SAM24407128, replicate 1, scRNASeq

value: Lung


title: SAM24407128, replicate 2, scRNASeq

value: Carcinoma Non-Small Cell


title: SAM24407127, replicate 2, scRNASeq

value: AMG-510 1.5um + TEADi 500nm


title: B-MDL119_v3_9418

value: Subject

value: After

value: 61 years


title: Rescue, clone29, SR2

value: self-renewal (SR)


title: B-MDL129_v1_111518

value: 56 years


title: SAM24407127, replicate 1, scRNASeq


title: 11H_M_2849


title: 11H_M_2848


title: A-MDL117_v1_61418

value: male

value: 53 years


title: Rescue, clone29, SR1


title: 11H_M_2847


title: SAM24407124, replicate 1, scRNASeq

value: Day 15


title: A-MDL107_v3_61318

value: saliva

value: normal

value: Control


title: Rescue, clone29, PD2

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)


title: 11H_M_2846


title: A-MDL101_v3_62018

value: 69 years


title: SAM24407123, replicate 2, scRNASeq

value: Lung


title: A-MDL135_v2_21519

value: Midpoint


title: Rescue, clone29, PD1


title: SAM24407123, replicate 1, scRNASeq

value: Carcinoma Non-Small Cell


title: 11H_M_2844


title: Rescue, clone2, SR2


title: 11H_M_2845


title: SAM24407122, replicate 2, scRNASeq


title: 11H_M_2843


title: A-MDL105_v2_43018


title: B-MDL126_v2_11918

value: Subject

value: 62 years


title: SAM24407122, replicate 1, scRNASeq


title: A-MDL118_v1_61818

value: Before

value: 50 years


title: Rescue, clone2, PD2


title: SAM24407121, replicate 3, scRNASeq

value: Baseline

value: Day 0


title: Rescue, clone2, PD1


title: Rescue, clone2, SR1

value: self-renewal (SR)


title: B-MDL121_v2_10218

value: male

value: 53 years


title: 11H_M_2842


title: 11H_M_2841


title: B-MDL112_v3_7918

value: saliva

value: normal

value: After

value: 51 years


title: Rescue, 172, B3, SR2

value: mouse trophoblast stem cells (mTSCs)

value: TSGFP


title: SAM24407121, replicate 1, scRNASeq

value: Lung


title: SAM24407121, replicate 2, scRNASeq

value: Carcinoma Non-Small Cell


title: 11H_M_2840


title: Rescue, 172, B3, SR1


title: OVCAR8_DMSO_rep3

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-10-10, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Ovary

extract_protocol:
Total RNA
TrueSeq Stranded Total RNA
Dual index

value: Ovary

value: Epithelial cell

value: DMSO


title: B-MDL124_v2_10518

value: Subject

value: Midpoint

value: 54 years


title: 11H_M_2839


title: OVCAR8_DMSO_rep2


title: B-MDL142_v1_61119

value: Before


title: 11H_M_2838


title: OVCAR8_DMSO_rep1


title: B-MDL132_v3_21319

value: male

value: 60 years


title: 11H_M_2837


title: Rescue, 172, B3, PD1

value: 24h differentiation with PD (PD)


title: A-MDL101_v1_41318

value: saliva

value: normal

value: Control

value: 69 years


title: 11H_M_2836


title: OVCAR8_GNE7883_rep3


title: OVCAR8_GNE7883_rep2


title: A-MDL127_v2_111318

value: 66 years


title: ErfKO, clone29, PD2

value: mouse trophoblast stem cells (mTSCs)

value: ErfKO


title: 11H_M_2834


title: OVCAR8_GNE7883_rep1

value: Ovary


title: 11H_M_2835


title: B-MDL112_v1_5718

value: 51 years


title: B-MDL109_v3_62118

value: After

value: 67 years


title: ErfKO, clone2, SR2

value: self-renewal (SR)


title: OVCAR8_Cpd3_rep3

value: Epithelial cell

value: Compound 3


title: OVCAR8_Cpd3_rep2


title: 11H_M_2833


title: B-MDL114_v2_62218

value: male

value: Subject

value: Midpoint

value: 58 years


title: ErfKO, clone2, SR1


title: 11H_M_2831


title: OVCAR8_Cpd3_rep1


title: B-MDL142_v2_71619

value: saliva

value: normal

value: 54 years


title: A-MDL134_v2_21219

value: Control

value: 65 years


title: OVCAR8_Cpd2_rep3

value: Compound 2


title: 11H_M_2830


title: Rescue, 172, B3, PD2

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)

value: TSGFP


title: ErfKO, clone29, SR1

value: ErfKO


title: ErfKO, clone29, SR2

value: self-renewal (SR)


title: OVCAR8_Cpd2_rep2

value: Ovary

value: Epithelial cell


title: ErfKO, clone2, PD2


title: A-MDL123_v1_82218

value: male

value: Before

value: 66 years


title: ErfKO, clone2, PD1


title: ErfKO, clone29, PD1


title: 11H_M_2829


title: A-MDL118_v3_81718

value: After

value: 50 years


title: 11H_M_2828


title: OVCAR8_Cpd2_rep1


title: 11H_M_2827


title: Empty, 171, B3, SR1


title: 11H_M_2832


title: B-MDL143_wd_7119

value: saliva

value: normal

value: Subject

value: 72 years


title: Empty, 171, B3, PD2


title: A-MDL136_v1_11519

value: Control

value: 58 years


title: Empty, 171, B3, PD1

value: mouse trophoblast stem cells (mTSCs)

value: 24h differentiation with PD (PD)


title: 11H_M_2825


title: OVCAR8_Cpd4_rep1

value: Compound 4


title: A-MDL111_v2_53118

value: Midpoint

value: 64 years


title: 8_BATFKO2_Th17_stim

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description:
RNA-seq
7_BATFKO_Th17_stim.bw

data_processing:
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build mm9 using Tophat2 (version 2.0.12). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: mm9
Supplementary_files_format_and_content: bw

source_name: CD4 T cell

growth_protocol: naïve CD4+ T cells isolated from spleen/lymph nodes were actiated with 2 ug/ml anti-CD3 and 0.5 ug/ml anti-CD28

extract_protocol: RNA extraction using miRNeasy Mini Kit (Qiagen)

treatment_protocol: Naïve cells were activated under Th17 culture conditions (20 ng/ml IL-6; 5 ng/ml human TGFb; 10 ng/ml IL-1b, 10 ug/ml anti-IL-4, and 10 ug/ml anti-IFNg) for 5 days.

value: activated CD4 T cells

value: spleen and lymph nodes

tag: genotype

value: wild-type


title: B-MDL103_v3_6418

value: male

value: 56 years


title: HCC1576_DMSO_rep3

source_name: Adrenal

tag: tissue

value: Adrenal

value: Epithelial cell

value: DMSO


title: 7_BATFKO1_Th17_stim

description:
RNA-seq
7_BATFKO_Th17_stim.bw


title: 11H_M_2824


title: HCC1576_DMSO_rep2

tag: cell line


title: B-MDL119_v1_7318

value: saliva

value: normal

value: Subject

value: Before

value: 61 years


title: Empty, 171, B3, SR2

tag: cell type

value: mouse trophoblast stem cells (mTSCs)

value: self-renewal (SR)

value: TSGFP


title: 11H_M_2822


title: HCC1576_DMSO_rep1

tag: treatment


title: 6_WT2_Th17_stim

description:
RNA-seq
5_WT_Th17_stim.bw


title: A-MDL134_v3_31319

value: Control

value: After

value: 65 years


title: A-MDL140_v2_6619

value: Midpoint

value: 64 years


title: HCC1576_GNE7883_rep3


title: 5_WT1_Th17_stim

description:
RNA-seq
5_WT_Th17_stim.bw

value: activated CD4 T cells

value: spleen and lymph nodes

value: wild-type


title: 4_BATFKO2_Th17_us

description:
RNA-seq
3_BATFKO_Th17_us.bw


title: A-MDL102_v1_32218

value: male

value: 54 years


title: 11H_M_2823


title: OVCAR8_Cpd4_rep3

value: Ovary

value: Epithelial cell

value: Compound 4


title: 11H_M_2821


title: 3_BATFKO1_Th17_us

description:
RNA-seq
3_BATFKO_Th17_us.bw


title: 11H_M_2826


title: OVCAR8_Cpd4_rep2


title: HCC1576_GNE7883_rep2

value: Adrenal


title: A-MDL106_v3_6518

value: saliva

value: normal

value: 50 years


title: 11H_M_2819


title: 2_WT2_Th17_us

description:
RNA-seq
1_WT_Th17_us.bw


title: HCC1576_Cpd3_rep3

value: Compound 3


title: 11H_M_2818


title: 1_WT1_Th17_us

description:
RNA-seq
1_WT_Th17_us.bw


title: HCC1576_Cpd3_rep2


title: B-MDL116_v2_71218

value: Subject

value: 58 years


title: 11H_M_2817


title: A-MDL135_v1_11019

value: Control

value: Before

value: 61 years


title: 54_D5_Th17_STAT5cKO2_Runx1

description:
53_D5_Th17_STAT5cKO_Runx1.bw
Runx1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

data_processing:
fastq QC
remove adapter: trim_galore v0.4.1
mapping: Bowtie1 (v1.1.2)
filter/remove duplicates: samtools v0.1.19
peak-calling: MACS2 v.2.1.0
normalization/tagcount/bedgraph: HOMER v4.9.0
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using HOMER

extract_protocol:
Cells (5-20 x 106) were cross-linked for 10 min with 1% formaldehyde, quenched with Glycine, and washed. Cell pellets were resuspended in lysis buffer, and homogenized. Nuclei were resuspended in RIPA buffer and sonicated to a size range of 200-600 bp using Qsonica. Cells were pelleted, and RIPA buffer was added to supernatant to 1 ml. Appropriate antibody coupled to Dynabeads M-280 Sheep anti-rabbit IgG  was added to the mix. The immunocomplexes were washed 5X with LiCl solution.  Supernatants were collected, incubated at 65C overnight, and immunoprecipiated DNA were purified using MinElute columns (Qiagen)
Immunoprecipiated DNA was used to prepare library using NEBNext Ultra II DNA library prep kit and NEBNext Multiplex Oligos for Illumina (NEB). ChIP-seq libraries were sequenced with single-end 50 bp using Illumina HiSeq 2500.

value: activated CD4 T cells

value: spleen and lymph nodes


title: A-MDL138_v2_52219

value: male

value: Midpoint


title: HCC1576_Cpd3_rep1


title: 53_D5_Th17_STAT5cKO1_Runx1

value: wild-type


title: HCC1576_Cpd2_rep3

value: Epithelial cell

value: Compound 2


title: 11H_M_2816


title: 11H_M_2815


title: B-MDL109_v1_41918

value: 67 years


title: 51_D5_Th17_Th17_D5_WT1_Runx1

description:
51_D5_Th17_WT_Runx1.bw
Runx1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2814


title: HCC1576_Cpd2_rep1

value: Adrenal


title: A-MDL125_v3_12418

value: saliva

value: normal

value: After

value: 65 years


title: B-MDL103_v2_5218

value: Subject

value: 56 years


title: HCC1576_Cpd2_rep2


title: HCC1576_GNE7883_rep1


title: 50_D5_Th17_STAT5cKO2_Ets1

description:
49_D5_Th17_STAT5cKO_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2820


title: 11H_M_2748


title: HCC1576_Cpd4_rep3

value: Compound 4


title: 49_D5_Th17_STAT5cKO1_Ets1


title: HCC1576_Cpd4_rep2


title: A-MDL113_v1_5818

value: Control

value: Before

value: 70 years


title: 11H_M_2747


title: 48_D5_Th17_WT2_Ets1

description:
47_D5_Th17_WT_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: A-MDL101_v2_52118

value: male

value: Midpoint

value: 69 years


title: A-MDL136_v3_31919

value: 58 years


title: 52_D5_Th17_Th17_D5_WT2_Runx1

value: wild-type


title: B-MDL126_v1_10818

value: saliva

value: 62 years


title: 11H_M_2744


title: 44_D5_Th17_WT2_H3K27ac

description:
43_D5_Th17_WT_H3K27ac.bw
H3K27ac ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: A-MDL133_v1_121318

value: normal

value: 57 years


title: 45_D5_Th17_STAT5cKO1_H3K27ac

description:
45_D5_Th17_STAT5cKO_H3K27ac.bw
H3K27ac ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2745


title: 11H_M_2813


title: B-MDL142_v3_81319

value: Subject

value: After

value: 54 years


title: H226_GNE7883_rep3

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline v1.
Reads were trimmed of adapters by cutadapt (version 1.9.1) and mapped to hg38 by Bowtie2 (version 2.2.6). Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand. TagAlign files were used to call peaks using MACS2 (version 2.1.0).  Peaks with p<1e-6 were retained for differential analysis.
Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand. TagAlign files were used to call peaks using MACS2 (version 2.1.0).  Peaks with p<1e-6 were retained for differential analysis.
TagAlign files were used to call peaks using MACS2 (version 2.1.0).  Peaks with p<1e-6 were retained for differential analysis.

source_name: Pleura

extract_protocol: none provided

value: Pleura


title: H226_GNE7883_rep2


title: 43_D5_Th17_WT1_H3K27ac


title: B-MDL110_v1_42018

value: Before

value: 64 years


title: H226_DMSO_rep3

value: DMSO


title: H226_DMSO_rep2


title: 11H_M_2741


title: 11H_M_2740


title: 42_D5_Th17_STAT5cKO2_H3K4me3

description:
41_D5_Th17_STAT5cKO_H3K4me3.bw
H3K4me3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: H226_DMSO_rep1


title: A-MDL105_v3_52518

value: male

value: Control

value: 61 years


title: 11H_M_2746


title: 47_D5_Th17_WT1_Ets1

value: wild-type


title: 41_D5_Th17_STAT5cKO1_H3K4me3


title: B-MDL122_v1_81518

value: saliva

value: 58 years


title: B-MDL108_v2_52118

value: normal

value: Midpoint

value: 51 years


title: H226_GNE7883_rep1


title: 46_D5_Th17_STAT5cKO2_H3K27ac


title: 11H_M_2743


title: A-MDL138_v1_41919

value: 50 years


title: 11H_M_2737


title: 40_D5_Th17_WT2_H3K4me3

description:
39_D5_Th17_WT_H3K4me3.bw
H3K4me3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2736


title: 11H_M_2739


title: 11H_M_2738


title: A-MDL117_v2_72318

value: 53 years


title: 39_D5_Th17_WT1_H3K4me3


title: 38_D5_Th17_BatfKO1_H3K27ac

description:
37_D5_Th17_BatfKO_H3K27ac.bw
H3K27ac ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2742


title: 37_D5_Th17_BatfKO1_H3K27ac


title: 11H_M_2735


title: HCE-T cells, CXCR4-KO_2

city: Guangzhou

first: Keming

last: Yu

address: No.7 Jinsui Road

country: China

institute: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
ACGT101-miR (LC Sciences, Houston, Texas, USA)
CASAVA 1.8
Sequenced using Illumina Hiseq2000/2500, with a single-end 1X50bp read length.
Inter-sample reproducibility analysis consisted of Pearson correlation analysis and Principal component analysis.
The Rfam database and Repbase were selected to annotate the small RNA sequences obtained by sequencing.
Assembly: hg38
Supplementary files format and content: csv file includes the name and sequence of miRNA, and raw count for each Sample

source_name: HCE-T cells

growth_protocol: HCE-T cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS), 5μg/mL insulin, 5 μg/mL epidermal growth factor.

extract_protocol:
TRIzol Reagent was used to isolate total RNA from cells (Invitrogen, Carlsbad, CA).
RNA libraries for RNA-seq were prepared using TruSeq Small RNA Sample Prep Kits(llumina, San Diego,USA) following manufacturer's protocols.

treatment_protocol: The hypoxic stimulation of the HCE-T cells was induced by culturing in the mixing of 5% CO2, 1% O2, and 94% N2 at 37 °C in a humidified atmosphere for 48 hours.

tag: biological replicates

value: biol rep 2

value: HCE-T cells

value: epithelial cell

value: hypoxic


title: HCE-T cells, CXCR4-KO_1

value: biol rep 1


title: HCE-T cells, CXCR4-KO_3

value: biol rep 3


title: HCE-T cells, wild-type_3


title: HCE-T cells, wild-type_2


title: B-MDL114_v1_51818

value: male

value: Subject

value: Before


title: HCE-T cells, wild-type_1


title: 11H_M_2734

tag: brain region


title: 36_D5_Th17_WT2_H3K27ac

description:
35_D5_Th17_WT_H3K27ac.bw
H3K27ac ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes

value: wild-type


title: A-MDL115_v1_53018

value: saliva

value: normal

value: Control

tag: age

value: 61 years


title: 35_D5_Th17_WT1_H3K27ac

tag: strain


title: A-MDL140_v3_7519

value: After

value: 64 years


title: 34_D5_Th17_BatfKO2_H3K4me3

description:
33_D5_Th17_BatfKO_H3K4me3.bw
H3K4me3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: RNA_Human_BA23_H1

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
All_Species_UMI_Count_Matrix_snRNAseq.mtx
All_Species_UMI_Count_Matrix_MetaData.txt
All_Species_UMI_Count_Matrix_Genes.txt
All_Species_UMI_Count_Matrix_Barcodes.txt
Seurat_Astrocyte_RNA.RDS
Seurat_Excitatory_RNA.RDS
Seurat_Inhibitory_RNA.RDS
Seurat_Microglia_RNA.RDS
Seurat_OPCOli_RNA.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger 3.1.0)
Chimpanzee, macaque reads were mapped to human (CrossMap)
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed expression matrix: mtx files, gene and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol:
Nuclei for snRNA-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.

value: brain

value: Brodmann Area 23

tag: Sex

value: F

tag: molecule subtype

value: nuclear RNA


title: B-MDL121_v3_103018

value: 53 years


title: 11H_M_2733


title: 11H_M_2732


title: B-MDL128_v2_121918

value: male

value: Midpoint

value: 50 years


title: B-MDL116_v3_8918

value: Subject

value: 58 years


title: Human_BA23_H1

description:
Human_Count_Matrix_snATACseq_Barcodes.txt
Human_Count_Matrix_snATACseq_Genes.txt
Human_Count_Matrix_snATACseq_MetaData.txt
Human_Count_Matrix_snATACseq.mtx
Seurat_Astrocyte_ATAC_Human.RDS
Seurat_Excitatory_ATAC_Human.RDS
Seurat_Inhibitory_ATAC_Human.RDS
Seurat_Microglia_ATAC_Human.RDS
Seurat_OPCOli_ATAC_Human.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger ATAC 1.1.0)
Supplementary_files_format_and_content: Read duplicates were removed (picard MarkDuplicates)
Peak calling (macs2 --nomodel, --keep-dup all, extsize 200, --shift –100 )
Common peak identification across samples and species (Refer to supplementary methods)
Peak-cell matrix generation (custom scripts)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed binarized peak-cell matrix: mtx file, peak and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

extract_protocol:
Nuclei for snATAC-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue as previously described: https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-6t8herw
Droplet-based single-nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library kit (1000110, 10x Genomics) according to the manufacturer’s protocols. Libraries were sequenced using an Illumina NovaSeq 6000.


title: Human_BA23_H2

value: M


title: 11H_M_2731


title: 32_D5_Th17_WT2_H3K4me3

description:
31_D5_Th17_WT_H3K4me3.bw
H3K4me3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes

value: wild-type


title: 33_D5_Th17_BatfKO1_H3K4me3


title: 31_D5_Th17_WT1_H3K4me3


title: A-MDL120_v2_82118

value: saliva

value: normal

value: Control

value: 61 years


title: B-MDL104_v1_32618

value: Before


title: P60, deaf, base, rep1

type: RNA

city: Iowa City

first: Steven

middle: Haym

last: Green

state: Iowa

address: 143 Biology Building

department: Biology

institute: University of Iowa

description:
P60DB1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

hyb_protocol: Labeled cDNA was hybridized for 20 hours to Roche NimbleGen HD2 rat gene expression arrays. Each biological replicate was analyzed in triplicate (3 technical replicates).

scan_protocol: Arrays were scanned on an Axon GenePix 4200A microarray scanner (Molecular Devices).

data_processing:
Pair files were generated and Lasergene ArrayStar (version 17, DNASTAR) was used for noise subtraction and RMA quantile normalization. Normalized signal intensities were used to calculate fold changes between conditions.
RMA-normalized-data_all-genes.txt is represented in the Data table (represents the normalized signal intensities for all genes present on the microarray).
RMA-normalized-data_expr-only.txt is linked as a supplementary file on the Series record (represents the normalized signal intensities for only the genes we considered to be expressed).

organism: Rattus norvegicus

source_name: P60 deaf spiral ganglion, basal half

label_protocol: cDNA was labeled using Cy3-coupled random nonamers (Roche NimbleGen).

growth_protocol: Sprague-Dawley rats from our breeding colony or from pregnant dams purchased from Envigo were used. Rats of both sexes were used. The day of birth was designated as P0.

extract_protocol: The Rneasy mini-kit (Qiagen) was used to extract total RNA from the isolated spiral ganglia. RNA was amplified (3-4X) using an Ambion Message Amp II kit. cDNA was then synthesized using a SuperScript II Reverse Transcriptase Second Strand kit.

treatment_protocol: Male and female Sprague-Dawley rats were injected with kanamycin (400 mg/kg, i.p.) once daily from P8-P16. Cochleae were collected from injected and littermate control (uninjected) rats at P32 or P60. Temporal bones were rapidly removed and placed in ice-cold phosphate-buffered saline, pH 7.4 (PBS) for dissection. The bony capsule and spiral ligament were dissected away from the cochlea. The remaining tissue was divided into apical and basal portions and the organ of Corti was separated from the spiral ganglion. Four to six ganglia were used for each biological replicate.

value: Sprague-Dawley

tag: condition

value: deaf

value: spiral ganglion

tag: cochlear location

value: base


title: 11H_M_2728


title: 11H_M_2730


title: B-MDL108_v1_41618

tag: gender

value: male

tag: sample type

value: 51 years


title: 11H_M_2729


title: 30_D5_Th17_BatfKO2_H3K27me3

description:
29_D5_Th17_BatfKO_H3K27me3.bw
H3K27me3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2727


title: B-MDL130_v1_111618

tag: disease state

tag: individual

value: Subject

value: 65 years


title: 29_D5_Th17_BatfKO1_H3K27me3

tag: genotype


title: 28_D5_Th17_WT2_H3K27me3

description:
27_D5_Th17_WT_H3K27me3.bw
H3K27me3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

tag: tissue


title: P60, hearing, base, rep1

description:
P60HB1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P60 hearing spiral ganglion, basal half

value: hearing


title: 11H_M_2726


title: A-MDL102_v3_52518

tag: timepoint (intervention)

value: After

value: 54 years


title: 27_D5_Th17_WT1_H3K27me3

value: activated CD4 T cells

value: spleen and lymph nodes

value: wild-type


title: B-MDL144_v2_72219

value: saliva

value: normal

value: Midpoint

value: 57 years


title: P60, hearing, apex, rep1

description:
P60HA1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P60 hearing spiral ganglion, apical half

value: Sprague-Dawley

value: apex


title: 11H_M_2725


title: P60, deaf, apex, rep1

description:
P60DA1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P60 deaf spiral ganglion, apical half

value: deaf

value: spiral ganglion


title: 26_D5_Th17_BatfKO2_IL6_STAT3

description:
25_D5_Th17_BatfKO_IL6_STAT3.bw
STAT3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 25_D5_Th17_BatfKO1_IL6_STAT3


title: A-MDL127_v1_10918

value: male

value: Control

value: Before

value: 66 years


title: 11H_M_2723


title: A-MDL137_v3_32619

value: After

value: 72 years


title: P32, deaf, base, rep1

description:
P32DB1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 deaf spiral ganglion, basal half

value: base


title: 24_D5_Th17_WT2_IL6_STAT3

description:
23_D5_Th17_WT_IL6_STAT3.bw
STAT3 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: B-MDL109_v2_52418

value: saliva

value: Subject

value: 67 years


title: HCC1576_Cpd4_rep1

value: Adrenal

tag: cell line

tag: cell type

value: Epithelial cell

value: Compound 4


title: 11H_M_2722


title: B-MDL124_v1_83118

value: normal

value: 54 years


title: 11H_M_2721


title: 23_D5_Th17_WT1_IL6_STAT3

value: wild-type


title: scl5 scl21 pat1 root tips SCLs_bleomycin_R2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

data_processing:
Illumina CASAVA software used for basecalling.
Paired-end reads were trimmed for adaptor sequences and aligned to the Araport11 exome using Salmon v0.9.1.
Transcript quantification was also performed by Salmon v0.9.1.
Assembly: Araport11 exome
Supplementary files format and content: tab-delimited text files generated from Salmon quantification, contain length of transcript in nucleotides, computed effective length, transcripts per million (TPM) and number of reads.

organism: Arabidopsis thaliana

source_name: scl5 scl21 pat1 root tips

growth_protocol: For each sample, approximately 100 Col-0 seeds or 100 scl5 scl21 pat1 seeds were sown on top of a nylon mesh on squared plates holding 1/2 MS medium and 1% agar.

extract_protocol:
0.2cm root tips were isolated and frozen in liquid nitrogen. RNA was extracted using QIAGEN Rneasy Plant Mini kit.
Libraries were prepared according to Illumina's instructions accompanying the NEBNext® UltraTM RNALibrary Prep Kit.

treatment_protocol: Seven days after sowing, the nylon mesh was transferred to either control 1/2 MS medium (control samples) or to 1/2 MS medium containing 0.5 ug/ml Bleomycin (bleomycin samples).

value: root tips

tag: strain/line

value: scl5 scl21 pat1

tag: treatment

value: 24h 0.5ug/ml bleomycin


title: P32, hearing, base, rep1

description:
P32HB1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 hearing spiral ganglion, basal half

value: Sprague-Dawley

tag: age

value: hearing

value: spiral ganglion


title: P32, hearing, apex, rep1

description:
P32HA1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 hearing spiral ganglion, apical half

tag: strain

value: apex


title: scl5 scl21 pat1 root tips SCLs_bleomycin_R3


title: scl5 scl21 pat1 root tips SCLs_bleomycin_R1


title: 22_D5_Th17_BatfKO2_IL2_STAT5

description:
21_D5_Th17_BatfKO_IL2_STAT5.bw
STAT5 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: 11H_M_2720

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: 21_D5_Th17_BatfKO1_IL2_STAT5


title: 11H_M_2719


title: A-MDL123_v3_102418

value: male

value: saliva

value: Control

value: After

value: 66 years


title: scl5 scl21 pat1 root tips SCLs_control_R3

value: control


title: 20_D5_Th17_WT2_IL2_STAT5

description:
19_D5_Th17_WT_IL2_STAT5.bw
STAT5 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: B-MDL119_v2_8718

value: normal

value: Subject

value: Midpoint

value: 61 years


title: scl5 scl21 pat1 root tips SCLs_control_R2

value: root tips

value: scl5 scl21 pat1


title: 11H_M_2724


title: 19_D5_Th17_WT1_IL2_STAT5

value: wild-type


title: P32, deaf, apex, rep1

description:
P32DA1
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 deaf spiral ganglion, apical half

value: Sprague-Dawley

value: deaf

value: spiral ganglion


title: scl5 scl21 pat1 root tips SCLs_control_R1


title: 11H_M_2717


title: 11H_M_2718


title: A-MDL105_v1_32618

source_name: saliva

value: Before


title: 11H_M_2716


title: B-MDL108_v3_61918

value: male

value: 51 years


title: B-MDL121_v1_72418

value: saliva

value: 53 years


title: A-MDL137_v1_12219

value: Control

value: 72 years


title: 17_D5_Treg_WT1_Runx1

description:
17_D5_Treg_WT_Runx1.bw
Runx1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: 16_D5_Th1_WT2_Runx1

description:
15_D5_Th1_WT_Runx1.bw
Runx1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 11H_M_2712


title: Col-0 root tips Col_bleomycin_R2

source_name: Col-0 root tips

value: 24h 0.5ug/ml bleomycin


title: 15_D5_Th1_WT1_Runx1

source_name: CD4 T cell


title: 11H_M_2713


title: Col-0 root tips Col_control_R2

value: control


title: 13_D5_Treg_WT1_Ets1

description:
13_D5_Treg_WT_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: Col-0 root tips Col_control_R3

value: root tips


title: 14_D5_Treg_WT2_Ets1


title: A-MDL137_v2_22619

value: normal

value: Midpoint


title: 11H_M_2711


title: B-MDL139_v3_62519

value: Subject

value: After

value: 70 years


title: 11H_M_2709


title: 18_D5_Treg_WT2_Runx1

value: wild-type


title: Col-0 root tips Col_control_R1


title: 11_D5_Th1_WT1_Ets1

description:
11_D5_Th1_WT_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: 12_D5_Th1_WT2_Ets1


title: B-MDL128_v1_111318

value: male

value: Before

value: 50 years


title: 11H_M_2715


title: Col-0 root tips Col_bleomycin_R3


title: UTSW-354 HPLM RNAseq

middle: G

last: McFadden

state: Texas

address: 5323 Harry Hines Blvd, K3.219

department: Departments of Internal Medicine and Biochemistry

data_processing:
Trim galore was used for quality and adapter trimming
Qualities of RNA-sequencing libraries were estimated by mapping the reads onto human transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie v2.3.4.3
STAR v2.7.2b was employed to align the reads onto the human genome
SAMtools was employed to sort the alignments
HTSeq Python package was employed to count reads per gene
FPKM values were calculated by a custom Perl script
Assembly: Ensembl 89

molecule: polyA RNA

growth_protocol: Cells were plated directly into 60mm TC dishes and allowed to adhere overnight. Cells were harvested the following day at approximately 80-90% confluence.

extract_protocol:
Media was removed, cells were rinsed one time with PBS, and 500 uL of TRIzol was added to each plate. Cells were lysed by pipetting up and down several times before total RNA was isolated through chloroform extraction and alcohol precipitation.
Total RNA was submitted to BGI Genomics for isolation of polyA RNAs, library preparation, and sequencing.

value: Thyroid cancer cell line


title: TPC-1 HPLM RNAseq


title: 11H_M_2708


title: A-MDL118_v2_72718

value: saliva

value: Control


title: Col-0 root tips Col_bleomycin_R1


title: A-MDL120_v1_71818

value: 61 years


title: 9_D5_Th17_BatfKO1_Runx1

description:
9_D5_Th17_BatfKO_Runx1.bw
Runx1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: 11H_M_2707


title: B-MDL114_v3_72018

value: 58 years


title: A-MDL107_v1_41018

value: 53 years


title: 10_D5_Th17_BatfKO2_Runx1


title: 11H_M_2710


title: MDAPCa2a. ACP-coating. 100 mM DHT Replicate 2

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

data_processing:
BBDuk tool (https://github.com/kbaseapps/BBTools), trimming adapters (ktrim=r k=23 mink=11 hdist=1), and low quality reads (lower than 28: "qtrim=r trimq=28")
STAR aligner (https://github.com/alexdobin/STAR) with (‘--outFilterScoreMinOverLread’ and ‘ –outFilterMatchNminOverLread’ parameters set to 0.2)
HTSeq-Counts (https://github.com/simon-anders/htseq).
Assembly: hg19
Supplementary files format and content: PCa_ACP_RNAseq.csv. Matrix table includes raw counts, genome wide for all experimental conditions in the study

source_name: Prostate epithelium. Bone metastatic

growth_protocol:
RWPE was cultured in keratinocyte SFM, supplemented with EGF and bovine pituitary extract (Gibco 17005042)
LNCaP media was composed of RPMI (Gibco, 11875119) supplemented with 10% FBS (Corning 35-010-CV), glucose (Corning, 25037CI), HEPES (Gibco, 15630080)  and sodium pyruvate (Gibco, 11360070) to match the concentrations suggested by ATCC (4.5 g/L glucose, 2.383 g/L HEPES and 0.11 g/L sodium pyruvate)
VCaP culture was 10% FBS, in DMEM: F12 Ham 1:1 basal media.
MDAPCa2a were cultured on BRFF-HPC1 base media (Athena Biologicals) supplemented with 20% FBS. These cells were require coating of plastic surfaces with FNC coating mix (Athena Biologicals) (Not used in calcium surfaces)
All cell culture media was supplemented with 1X penicillin/Streptomycin (Gibco15140122)

extract_protocol:
RNA was purified using the Rneasy plus kit (Quiagen 74034).
RNA-seq libraries were generated by Genewiz South Plainfield, NJ) using PolyA selection for mRNA species

treatment_protocol:
For plastic experiments two T75 flasks of continuous cultured cells were passaged at a subuclture ratio of 1:3 into a) plastic -control media and b) plastic - charcoal dextran stripped FBS containing media and cultured for four days with one media change on day 2
For ACP experiments three T75 flasks of continuous cultured cells were passaged at a subuclture ratio of 1:3 into a) ACP coated plates -control media  b) ACP coated platesplastic - charcoal dextran stripped FBS containing media and c) ACP coated plates, containing charcoal dextran stripped FBS and supplemented with 100mM testosterone. Cells were cultured for four days with one media change on day 2

value: Prostate epithelium. Bone metastatic

value: ACP-coating. 100mM testosterone

tag: time

value: Day 4


title: 8_D5_Th17_WT2_Runx1

description:
7_D5_Th17_WT_Runx1.bw
Runx1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: NCI-237 HPLM RNAseq


title: 11H_M_2706


title: 11H_M_2705


title: A-MDL125_v2_11818

value: normal

value: Midpoint

value: 65 years


title: MDAPCa2a. ACP-coating. 100 mM DHT Replicate 1

tag: condition


title: 7_D5_Th17_WT1_Runx1

value: wild-type


title: B-MDL131_v3_2619

value: male

value: Subject

value: After

value: 56 years


title: MDAPCa2a. ACP-coating. Charcoal dextran stripped serum Replicate 2

value: ACP-coating Charcoal Dextran stripped serum


title: 6_D5_Th17_BatfKO2_Ets1

description:
5_D5_Th17_BatfKO_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)


title: A-MDL115_v2_7218

value: saliva

value: Control

value: 61 years


title: 11H_M_2704


title: 11H_M_2703


title: 5_D5_Th17_BatfKO1_Ets1

value: activated CD4 T cells

value: spleen and lymph nodes


title: MDAPCa2a. ACP-coating. Charcoal dextran stripped serum Replicate 1

value: Prostate epithelium. Bone metastatic


title: MDAPCa2a. Plastic. Charcoal dextran stripped serum. Replicate 2

value: Plastic. Charcoal Dextran stripped Serum


title: 11H_M_2702


title: B-MDL143_v1_61319

value: Before

value: 72 years


title: B-MDL103_v1_32318

value: normal


title: MDAPCa2a. Plastic. Charcoal dextran stripped serum. Replicate 1

value: Day 4


title: 4_D5_Th17_WT2_Ets1

description:
3_D5_Th17_WT_Ets1.bw
Ets1 ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: wild-type


title: 3_D5_Th17_WT1_Ets1


title: 11H_M_2699


title: B-MDL132_v1_121218

value: male

value: 60 years


title: A-MDL127_v3_121118

value: After

value: 66 years


title: MDAPCa2a. Plastic Control media Replicate 1

value: Plastic. Control Media

value: Continuous culture


title: 11H_M_2701


title: 11H_M_2697


title: TISKM4

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

data_processing:
For the digital samples processing we used Dropseq pipeline (version 2.5.1)
https://github.com/broadinstitute/Drop-seq/tags
Assembly: GRCh38
Supplementary files format and content: txt files with DEG for each sample

source_name: skin

growth_protocol: Cells were cultured in RPMI-1640 media supplemented with 10% FCS and incubated in a humidified atmosphere with 5% CO2 at 37°C. Untreated and fully resistant proliferative cells were passaged every 3 to 4 days. For drug-sensitive cells that undergo senescent-like phenotype under treatment medium was renewed every 3 to 4 days.

extract_protocol: scRNAseq - Dropseq method (Macosko et al., 2015)

treatment_protocol: NRAS-mutant melanoma cells were treated with combined 1µM CDK4/6 inhibitor Palbociclib and MEK inhibitor Binimetinib added in cell line specific 1xIC50 concentration. Cells were treated over a period of 33 days.

value: skin

value: cancer

value: NRAS Q61K

value: Binimetinib plus Palbociclib (33d)


title: 11H_M_2700


title: 2_D5_Th17_WT2_Batf

description:
1_D5_Th17_WT_Batf.bw
Batf ChIP-seq
rabbit anti-Batf (Schraml et al., 2010), rabbit anti-Ets1 (abcam, ab124282), rabbit anti-Runx1 (abcam, ab23980), rabbit anti-H3K27me3 (Millipore, 07-449), rabbit anti-H3K4me3 (Millipore, 07-473), rabbit anti-H3K27ac (abcam, ab4729), rabbit anti-STAT3 (Millipore, 06-596), rabbit anti-STAT5 (R&D, AF2168), and normal rabbit IgG (Millipore, 12-370)

value: activated CD4 T cells

value: spleen and lymph nodes


title: 1_D5_Th17_WT1_Batf


title: MDAPCa2a. Plastic Control media Replicate 2

value: Prostate epithelium. Bone metastatic


title: VCaP. ACP-coating. 100 mM DHT Replicate 2

value: VCaP

value: ACP-coating. 100mM testosterone


title: B-MDL112_v2_61118

value: saliva

value: normal

value: Subject

value: Midpoint

value: 51 years


title: A-MDL135_v3_31419

value: male

value: Control

value: After

value: 61 years


title: 11H_M_2698


title: B-MDL139_v1_42219

value: Before

value: 70 years


title: 11H_M_2696


title: VCaP. ACP-coating. 100 mM DHT Replicate 1

value: Day 4


title: A-MDL107_v2_51418

value: 53 years


title: 11H_M_2695


title: A-MDL141_v1_53119

value: 57 years


title: TISKM1

value: skin

value: cancer

value: NRAS Q61K

value: Untreated


title: VCaP. ACP-coating. Charcoal dextran stripped serum Replicate 2

value: VCaP

value: Prostate epithelium. Bone metastatic

value: ACP-coating Charcoal Dextran stripped serum


title: TISKM3

value: Binimetinib plus Palbociclib (4d)


title: TISKM2

value: Binimetinib plus Palbociclib (1d)


title: VCaP. ACP-coating. Charcoal dextran stripped serum Replicate 1


title: VCaP. ACP-coating. Control Media. Replicate 2

value: ACP-coating control media


title: B-MDL131_v2_1819

value: male

value: saliva

value: normal

value: Subject

value: Midpoint

value: 56 years


title: 11H_M_2694


title: B-MDL129_v2_122018


title: 11H_M_2693


title: TI44

value: NRAS Q61H

value: Binimetinib plus Palbociclib (33d)


title: VCaP. ACP-coating. Control Media. Replicate 1

value: Day 4


title: A-MDL125_v1_10418

value: Control

value: Before

value: 65 years


title: TI43

value: skin

value: cancer


title: VCaP. Plastic. Charcoal dextran stripped serum. Replicate 1

value: VCaP

value: Prostate epithelium. Bone metastatic

value: Plastic. Charcoal Dextran stripped Serum


title: 11H_M_2692


title: A-MDL133_v3_21419

value: male

value: After

value: 57 years


title: 11H_M_2691


title: 11H_M_2690


title: VCaP. Plastic Control media Replicate 2

value: Plastic. Control Media

value: Continuous culture


title: A-MDL106_v2_5418

value: saliva

value: normal

value: Midpoint

value: 50 years


title: TI42

value: NRAS Q61H

value: Binimetinib plus Palbociclib (1d)


title: TI41

value: Untreated


title: LNCaP. ACP-coating. 100 mM DHT Replicate 2

source_name: Prostate epitehlium. Lymph node metastatic

value: LNCaP

value: ACP-coating. 100mM testosterone

value: Day 4


title: TI28

value: skin

value: cancer

value: NRAS Q61L

value: Binimetinib plus Palbociclib (33d)


title: 11H_M_2689


title: TI27

value: Binimetinib plus Palbociclib (4d)


title: 11H_M_2688


title: LNCaP. ACP-coating. 100 mM DHT Replicate 1

value: Prostate epitehlium. Lymph node metastatic


title: 11H_M_2687


title: TI26


title: Islet-associated macrophages, high fat diet, 8

city: Oxford

first: Cecilia

last: Lindren

address: Old Road Campus

department: Big Data Institute

country: United Kingdom

institute: University of Oxford

data_processing:
FASTQC using default parameter
Trimgalore using default parameter
Star aligner
Rsem for count quatification
Assembly: Mus_musculus.GRCm38.85

source_name: Pancreatic islet

extract_protocol:
RNA was extracted using RNeasy mini kits
500pg of RNA was used for library preparation using the Ovation® RNA-Seq System V2

treatment_protocol: Mice were maintained on chow or high fat diets for 8 weeks

tag: Sex

value: Male

value: Pancreatic islet

value: Macrophage

value: 16-week old

value: Wild-type

value: High fat diet


title: Islet-associated macrophages, high fat diet, 7


title: 11H_M_2686


title: TI25


title: 11H_M_2685


title: LNCaP. ACP-coating. Charcoal dextran stripped serum Replicate 2

value: ACP-coating Charcoal Dextran stripped serum


title: Islet-associated macrophages, high fat diet, 6


title: Islet-associated macrophages, high fat diet, 5


title: 11H_M_2620


title: LNCaP. ACP-coating. Charcoal dextran stripped serum Replicate 1


title: TI23

value: MEL-JUSO


title: A-MDL111_v1_42618

tag: gender

value: male

value: saliva

value: normal

value: Control

value: Before

value: 64 years


title: VCaP. Plastic Control media Replicate 1

value: VCaP

value: Prostate epithelium. Bone metastatic

value: Plastic. Control Media

value: Continuous culture


title: LNCaP. ACP-coating. Control Media. Replicate 1

value: LNCaP

value: Prostate epitehlium. Lymph node metastatic

value: ACP-coating control media

value: Day 4


title: TI22

value: skin

value: cancer

value: NRAS Q61L

value: Binimetinib plus Palbociclib (1d)


title: TI21

value: MEL-JUSO

value: Untreated


title: Islet-associated macrophages, chow, 4

value: Male

value: Pancreatic islet

value: Macrophage

value: 16-week old

value: Wild-type

value: Chow diet


title: 11H_M_2619


title: LNCaP. Plastic. Charcoal dextran stripped serum. Replicate 1

value: Plastic. Charcoal Dextran stripped Serum


title: 11H_M_2618


title: 11H_M_2617


title: Islet-associated macrophages, chow, 2


title: TI24

value: Binimetinib plus Palbociclib (33d)


title: Islet-associated macrophages, chow, 1


title: UTSW-354 targeted screen HPLM final rep 2

data_processing:
Samples were demultiplexed
BWA was used to map the sequencing reads o the sgRNA sequences concatenated with 5' and 3' flanking sequences
Mapping reads were counted for each sgRNA using SAMtools v1.9 with the options "-F 2308 -q 1"
MAGeCK was used to determine the relative depletion and enrichment of genes in endpoint samples compared to initial samples

growth_protocol: For the genome-wide screen, approximately 270 x 10^6 NCI-237 and TPC-1 cells stably expressing Cas9 were transduced with the Brunello sgRNA library such that approximately 20-40% of cells survived puromycin selection. 48 hours after transduction, cells were selected in media containing 2 ug/mL puromycin and maintained in puromycin-containing media for 7 days. An initial timepoint of cells was collected and cells were subsequently cultured for approximately 12 population doublings, maintaining approximately 80 x 10^6 cells at each passage. For the targeted screen, approximately 8 x 10^6 NCI-237, TPC-1, and UTSW-354 cells stably expressing Cas9 that were cultured in either RPMI or HPLM were transduced with the targeted sgRNA library such that approximately 20-40% of cells survived puromycin selection. 48 hours after transduction, cells were selected in media containing 2 ug/mL puromycin and maintained in puromycin-containing media for 7 days. An initial timepoint of cells was collected and cells were subsequently cultured for approximately 14 population doublings, maintaining approximately 2 x 10^6 cells at each passage.

extract_protocol:
For the genome-wide screen, genomic DNA was prepared using the Qiagen Blood and Cell Culture DNA Maxi Kit. For the targeted screen, genomic DNA was prepared using the Zymo Quick-DNA Miniprep Kit.
For the genome-wide screen, sgRNA cassettes were amplified using 22 cycles of PCR amplification from approximately 300 µg genomic DNA (10 µg DNA/100 µL reaction) using 2X KAPA HiFi HotStart ReadyMix (Roche KK2602), a combination of 8 staggered P5 primers, and 1 unique P7 index primer per sample as described by the Broad Institute Genetic Perturbation Platform. For the targeted screen, sgRNA cassettes were amplified using 22 cycles of PCR amplification from approximately 12 µg genomic DNA (10 µg DNA/100 µL reaction) using 2X KAPA HiFi HotStart ReadyMix (Roche KK2602), a combination of 8 staggered P5 primers, and 1 unique P7 index primer per sample. The PCR products were purified using AMPure XP beads. PCR products were pooled and sequenced on an Illumina NextSeq 500 with 75 duty cycles.

value: Thyroid cancer cell line

value: HPLM


title: LNCaP. Plastic Control media Replicate 1

value: LNCaP

value: Prostate epitehlium. Lymph node metastatic

value: Plastic. Control Media

value: Continuous culture


title: LNCaP. ACP-coating. Control Media. Replicate 2

value: ACP-coating control media

value: Day 4


title: LNCaP. Plastic Control media Replicate 2


title: 11H_M_2616

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

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


title: UTSW-354 targeted screen HPLM initial rep 2


title: Ribo-seq MCMV 24hpi - Lactimidomycin - Rep 5

city: Wuerzburg

first: Florian

last: Erhard

address: Versbacher Straße 7

country: Germany

institute: Institute of Virology and Immunobiology, University of Wuerzburg

data_processing:
3' sequencing adapter sequence were removed from the 49 nt long reads using reaper 15.065
Barcode sequences (first 9 nt = 3 random bases followed by 4 bases of experiment specific barcodes followed by 2 random bases) were removed from all reads and stored for later use.
Bowtie 1.2 was used to align all reads to ribosomal rRNA and Mycoplasma. Reads mapped to ribosomal rRNA and Mycoplasma were discarded. The remaining reads were aligned to the mouse genome, Ensembl transcripts (v90), the MCMV genome (KY348373), and the MCMV transcripts (KY348373). Only reads with at most 3 mismatches were kept for further analyses.
The total number of unique sequences was taken as the conservative fragment count.
Mapped reads were further processed by PRICE 1.0.4 to identify open reading frames.
Assembly: GRCm38, KY348373
Supplementary files format and content: Tab separated file showing the read count of each open reading frame in each condition / time point. The processed file / PRICE output is decribed in detail here: https://github.com/erhard-lab/gedi/wiki/Price#using-the-output

source_name: NIH-3T3 Murine embryonic fibroblasts

growth_protocol: NIH-3T3 cells were cultured in DMEM supplements with 10% NCS and Pen-Strep, 100 IU/mL and 100µg/mL, respectively. Cells at passage 6 were infected at 80% confluency 24h after the last split.

extract_protocol:
Cells were snap frozen followed by cell lysis in presence of cycloheximide. Following removal of cell nuclei by centrifugation and stringent RNAse digest, ribosomes were pelleted through a sucrose cushion. Translated RNA fragments were recovered by size selection.
Translated RNA fragments were cloned following the protocol described by Stern-Ginossar N et al. Science 2012. rRNA depletion involved additional biotinylated oligos to improve depletion. To efficiently remove all biotinylated oligos complementary to specific rRNA sequences, two rounds of streptavidin depletion were performed. cDNA libraries were amplified by PCR and sequenced (HiSeq 50nt reads).

treatment_protocol: Cells were infected for 30 min with Smith strain MCMV at an MOI with centrifugal enhancement at 800g/30mins, followed by PBS wash and media replacement. Harringtonin (2µg/ml for for 30 min) or Lactimidomycin (50µM for 30 min) treatment was conducted prior to cell lysis to arrest ribosomes at start sites

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV, 24 h p.i.

tag: infection with

value: MCMV

tag: barcode

value: GGCA

tag: replicate

value: Replicate 5

tag: molecule type

value: Ribosome protected RNA fragments (29-30nt)

value: Lactimidomycin


title: 11H_M_2615


title: RWPE. ACP-coating. 100mM DHT Replicate 3

source_name: Prostate epithelium.  Non tumorogenic

value: RWPE

tag: tissue

value: Prostate epithelium.  Non tumorogenic

value: ACP-coating. 100mM testosterone


title: Ribo-seq MCMV 24hpi - Harringtonin - Rep 5

value: CGGA

value: Harringtonin


title: 11H_M_2614


title: Ribo-seq MCMV 6hpi - Harringtonin - Rep 5

value: MCMV, 6 h p.i.

value: CCGG


title: RWPE. ACP-coating. 100mM DHT Replicate 2

tag: cell line


title: UTSW-354 targeted screen RPMI final rep 2

tag: cell type

value: Thyroid cancer cell line

value: RPMI


title: 11H_M_2613


title: Islet-associated macrophages, chow, 3

value: Male

value: Pancreatic islet

value: Macrophage

value: 16-week old

tag: genotype

value: Wild-type

value: Chow diet


title: LNCaP. Plastic. Charcoal dextran stripped serum. Replicate 2

value: LNCaP

value: Prostate epitehlium. Lymph node metastatic

value: Plastic. Charcoal Dextran stripped Serum

value: Day 4


title: RWPE. ACP-coating. 100mM DHT Replicate 1

value: RWPE

value: Prostate epithelium.  Non tumorogenic

value: ACP-coating. 100mM testosterone


title: Ribo-seq MCMV 2hpi - Harringtonin - Rep 5

value: Immortalized embryonic fibroblasts

value: MCMV, 2 h p.i.

value: MCMV

value: CAAT

value: Replicate 5

value: Ribosome protected RNA fragments (29-30nt)

tag: treatment

value: Harringtonin


title: RWPE. ACP-coating. Control Media. Replicate 2

value: ACP-coating control media


title: UTSW-354 targeted screen RPMI initial rep 2

value: Thyroid cancer cell line

value: RPMI


title: 11H_M_2612

tag: age


title: UTSW-354 targeted screen RPMI final rep 1


title: UTSW-354 targeted screen HPLM final rep 1

value: HPLM


title: RWPE. ACP-coating. Control Media. Replicate 1


title: UTSW-354 targeted screen RPMI initial rep 1


title: 11H_M_2610

tag: strain


title: TPC-1 targeted screen HPLM final rep 2


title: RWPE. Plastic Control media. Replicate 2

value: Plastic. Control Media

value: Continuous culture


title: 11H_M_2611

tag: brain region


title: Ribo-seq MCMV 24hpi - Harringtonin - Rep 4

value: MCMV, 24 h p.i.

value: AATA

value: Replicate 4


title: 11H_M_2609


title: Ribo-seq MCMV 48hpi - Cycloheximide - Rep 4

value: MCMV, 48 h p.i.

value: TTAA

value: Cycloheximide


title: RWPE. Plastic Control media. Replicate 1

value: RWPE

value: Prostate epithelium.  Non tumorogenic

tag: time


title: UTSW-354 targeted screen HPLM initial rep 1


title: Ribo-seq MCMV 24hpi - Cycloheximide - Rep 4

value: Immortalized embryonic fibroblasts

value: MCMV

value: GGCA


title: TPC-1 targeted screen HPLM initial rep 2


title: Ribo-seq MCMV 12hpi - Cycloheximide - Rep 4

value: MCMV, 12 h p.i.

value: CGGA

value: Ribosome protected RNA fragments (29-30nt)


title: acc, stim, rep10

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

description:
column number 24
BBBD23

data_processing:
Raw reads were trimmed using cutadapt v1.10
Reads were aligned using STAR v2.5.3a
Gene counts were generated using HTSeq v0.6.1p1, with annotations from Ensembl v95
Differential expression analysis was conducted using DESeq2 v1.22.1
Assembly: mm10
Supplementary files format and content: csv file includes: raw Gene counts; normalized Gene counts; differential expression results with log2 fold change, nominal and adjusted p-values

source_name: brain,  anterior cingulate cortex

extract_protocol:
Total RNA was extracted from bulk ACC tissue with the QIAGEN RNeasy Mini Kit
RNA libraries for RNA-seq were prepared using the SMARTSeq v4 Ultra Low Input RNA kit for Sequencing (PN 091817, Takara Bio Europe, Saint-Germain-en-Laye, France) following manufacturer's protocols. Full length cDNAs were generated from 5ng of total RNA, with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase.

value: brain,  anterior cingulate cortex

value: bulk tissue

value: wildtype

value: 9 optogenetic stimulations of the BLA-ACC pathway


title: acc, stim, rep9

description:
column number 23
BBBD22


title: 11H_M_2607


title: acc, stim, rep8

description:
column number 22
BBBD21


title: TPC-1 targeted screen HPLM initial rep 1

value: Thyroid cancer cell line

value: HPLM


title: 11H_M_2606


title: 11H_M_2605


title: Ribo-seq Mock - Lactimidomycin - Rep 5

value: Mock

value: TTGT

value: Replicate 5

value: Lactimidomycin


title: Ribo-seq MCMV 6hpi - Harringtonin - Rep 4

value: MCMV, 6 h p.i.

value: CCAC

value: Replicate 4

value: Harringtonin


title: Ribo-seq MCMV 6hpi - Cycloheximide - Rep 4

value: Immortalized embryonic fibroblasts

value: MCMV

value: TGGC

value: Cycloheximide


title: TPC-1 targeted screen RPMI final rep 2

value: RPMI


title: acc, stim, rep7

description:
column number 21
BBBD20

value: brain,  anterior cingulate cortex

value: bulk tissue

value: wildtype


title: Ribo-seq MCMV 2hpi - Harringtonin - Rep 4

value: MCMV, 2 h p.i.

value: CCGG

value: Ribosome protected RNA fragments (29-30nt)


title: acc, stim, rep6

description:
column number 20
BBBD19

value: 9 optogenetic stimulations of the BLA-ACC pathway


title: 11H_M_2604


title: TPC-1 targeted screen RPMI initial rep 2

value: Thyroid cancer cell line


title: Ribo-seq MCMV 2hpi - Cycloheximide - Rep 4

value: CAAT


title: acc, stim, rep5

description:
column number 19
BBBD18


title: 11H_M_2603


title: TPC-1 targeted screen RPMI initial rep 1


title: acc, stim, rep4

description:
column number 12
BBBD11


title: Ribo-seq Mock - Harringtonin - Rep 4

value: Mock

value: TTGT


title: Ribo-seq Mock - Cycloheximide - Rep 4

value: GGTT

value: Replicate 4


title: NCI-237 targeted screen HPLM final rep 2

source_name: NCI-237 UTSW

value: NCI-237 UTSW

value: HPLM


title: 11H_M_2608


title: 11H_M_2601


title: 11H_M_2602


title: TPC-1 targeted screen HPLM final rep 1


title: NCI-237 targeted screen HPLM initial rep 2


title: acc, stim, rep3

description:
column number 11
BBBD10


title: Ribo-seq MCMV 48hpi - Cycloheximide - Rep 3

value: Immortalized embryonic fibroblasts

value: MCMV, 48 h p.i.

value: MCMV

value: AATA

value: Replicate 3

value: Cycloheximide


title: acc, stim, rep2

description:
column number 10
BBBD9

value: brain,  anterior cingulate cortex

value: bulk tissue

value: wildtype


title: Ribo-seq MCMV 24hpi - Harringtonin - Rep 3

value: MCMV, 24 h p.i.

value: CGGA

value: Ribosome protected RNA fragments (29-30nt)

value: Harringtonin


title: NCI-237 targeted screen HPLM final rep 1

value: Thyroid cancer cell line


title: acc, stim, rep1

description:
column number 9
BBBD8

value: 9 optogenetic stimulations of the BLA-ACC pathway


title: Ribo-seq MCMV 24hpi - Cycloheximide - Rep 3

value: CCAC


title: acc, ctrl, rep12

description:
column number 18
BBBD17

value: ctrl (no light)


title: Ribo-seq MCMV 12hpi - Cycloheximide - Rep 3

value: Immortalized embryonic fibroblasts

value: MCMV, 12 h p.i.

value: GGTC


title: NCI-237 targeted screen RPMI final rep 2

value: NCI-237 UTSW

value: RPMI


title: acc, ctrl, rep11

description:
column number 17
BBBD16


title: Ribo-seq MCMV 6hpi - Cycloheximide - Rep 3

value: MCMV, 6 h p.i.

value: MCMV

value: TGGC

value: Replicate 3

value: Cycloheximide


title: NCI-237 targeted screen RPMI initial rep 2


title: 11H_M_2596


title: TPC-1 targeted screen RPMI final rep 1


title: Ribo-seq MCMV 2hpi - Harringtonin - Rep 3

value: MCMV, 2 h p.i.

value: GGCG


title: acc, ctrl, rep9

description:
column number 15
BBBD14

value: brain,  anterior cingulate cortex

value: bulk tissue

value: wildtype


title: 11H_M_2595


title: Ribo-seq MCMV 2hpi - Cycloheximide - Rep 3

value: CAAT

value: Ribosome protected RNA fragments (29-30nt)


title: NCI-237 targeted screen RPMI final rep 1

value: Thyroid cancer cell line


title: NCI-237 targeted screen RPMI initial rep 1


title: Ribo-seq Mock - Cycloheximide - Rep 3

value: Immortalized embryonic fibroblasts

value: Mock

value: TTGT


title: acc, ctrl, rep8

description:
column number 14
BBBD13

value: ctrl (no light)


title: 11H_M_2600


title: 11H_M_2594


title: TPC-1 genome-wide screen final

value: RPMI


title: Ribo-seq MCMV 48hpi - Cycloheximide - Rep 2

value: MCMV, 48 h p.i.

value: MCMV

value: Replicate 2


title: 11H_M_2593


title: 11H_M_2592


title: acc, ctrl, rep6

description:
column number 8
BBBD6


title: TPC-1 genome-wide screen initial


title: 11H_M_2599


title: NCI-237 targeted screen HPLM initial rep 1

value: NCI-237 UTSW

value: HPLM


title: 11H_M_2598


title: Ribo-seq MCMV 24hpi - Cycloheximide - Rep 2

value: MCMV, 24 h p.i.

value: CCGG

value: Cycloheximide


title: NCI-237 genome-wide screen final


title: 11H_M_2597


title: acc, ctrl, rep5

description:
column number 7
BBBD5

value: brain,  anterior cingulate cortex

value: bulk tissue

value: wildtype


title: Ribo-seq MCMV 12hpi - Cycloheximide - Rep 2

value: MCMV, 12 h p.i.

value: GGCG

value: Ribosome protected RNA fragments (29-30nt)


title: NCI-237 genome-wide screen initial

value: Thyroid cancer cell line


title: 11H_M_2591


title: acc, ctrl, rep4

description:
column number 6
BBBD4

value: ctrl (no light)


title: acc, ctrl, rep10

description:
column number 16
BBBD15


title: 11H_M_2590


title: 11H_M_2589


title: Ribo-seq MCMV 2hpi - Cycloheximide - Rep 2

value: Immortalized embryonic fibroblasts

value: MCMV, 2 h p.i.

value: TTGT


title: D15-B6-BRA-AD

city: Kagoshima

first: Yuya

last: Tomioka

country: Japan

institute: Kagoshima University

data_processing:
The bcl2fastq v 2.20 was used for basecalling.
Raw data were applied to the bioinformatic pipeline, which includes quality control with FastQC v0.11.9 and MultiQC v1.12.
The QIAseq miRNA library kit adopts the Unique Molecular Indexes (UMIs) system, enabling unbiased and accurate quantification of mature miRNAs.
Original FASTQ files generated by the NextSeq were uploaded to the Qiagen GeneGlobe Data Analysis Center (https://geneglobe.qiagen.com) and aligned to the miRBase v21 (http://www.mirbase.org) and piRNABank (http://pirnabank.ibab.ac.in/).
All reads assigned to a particular miRNA or piRNA were counted and the associated UMIs were aggregated to count unique molecules.
A matrix of the UMI counts of miRNA or piRNA was subjected to downstream analyses using StrandNGS 4.0 software (Agilent Technologies, Santa Clara, CA).
The UMI counts were quantified using a Trimmed Mean of M-value (TMM) method. miRNAs were annotated against miRBase (Release 21), using R v3.6.2.
Assembly: Human hg38

source_name: brain metastases

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were constructed using the QIAseq™ miRNA Library Kit (Cat#331505, Qiagen, Hilden, Germany) according to the manufacturer’s protocols.

tag: disease state

value: lung adenocarcinoma

value: brain metastases


title: acc, ctrl, rep3

description:
column number 5
BBBD3


title: D14-B5-BRA-AD


title: acc, ctrl, rep2

description:
column number 4
BBBD2


title: 11H_M_2588


title: D13-B4-BRA-AD


title: Ribo-seq MCMV 6hpi - Cycloheximide - Rep 2

value: MCMV, 6 h p.i.

value: MCMV

value: CAAT

value: Replicate 2


title: acc, ctrl, rep1

description:
column number 3
BBBD1

value: brain,  anterior cingulate cortex


title: Ribo-seq MCMV 48hpi - Cycloheximide - Rep 1

value: MCMV, 48 h p.i.

value: TTAA

value: Replicate 1

value: Cycloheximide


title: Ribo-seq Mock - Cycloheximide - Rep 2

value: Mock

value: GGTT

value: Ribosome protected RNA fragments (29-30nt)


title: 11H_M_2587


title: D12-B3-BRA-AD


title: 11H_M_2586


title: Total RNA-seq Hindlimb (Pbx1/Pbx2 mutant; rep. 3)

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

data_processing:
Reads for each tissue were mapped against the mouse genome (mm10) using the Tophat 2 aligner (version 2.0.13) (PMID: 23618408) with default parameter settings except for setting the flag --no-coverage-search.
Expression levels for each tissue were initially quantified using htseq-count (PMID: 25260700).
Genome_build: mm10; iGenome transcripts
Supplementary_files_format_and_content: *.counts.txt, HTseq quantifications

source_name: embryonic hindlimb bud

growth_protocol: Mutant alleles were previously described and the conditions for genotyping were reported: conditional Pbx1 (PMID: 22560297), Pbx2 (PMID: 15169896), constitutive and conditional Hand2 (PMID: 20386744), Hoxb6Cre (PMID: 10686603).

extract_protocol:
Hindlimb buds from mutant and littermate controls were dissected individually at the indicated gestational days and snap frozen in dry ice. After genotyping of individual samples, each biological replicate consisted of one individual mutant or littermate embryo, with a total of 3 biological replicates per genotype. RNA was extracted using the RNeasy Plus Micro kit (Qiagen, #74034) and RNA quantification was performed using the Qubit RNA HS Assay Kit (Invitrogen, #Q32852). Quality control of input RNA was performed using the RNA 6000 Pico kit (Agilent, #5067–1513) on a 2100 Bioanalyzer (Agilent). All RNA samples used for library preparation had RIN>9.
RNA sequencing libraries were prepared from 100 ng of input RNA using the non-directional kit NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, #E7775) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490) to capture polyA RNAs. Library size and quality was checked using an Agilent 2100 Bioanalyzer with the High Sensitivity DNA kit (Agilent, #5067–4626), and library concentration was determined with the QuBit dsDNA HS Assay kit (Invitrogen, #Q32854). Libraries were normalized to 10 nM, pooled, and sequenced in an Illumina HiSeq 4000 to generate 50 base pair single-end reads.

treatment_protocol: None.

value: embryonic hindlimb bud

tag: developmental stage

value: gestational day e10.5

tag: library strand status

value: Unstranded


title: 11H_M_2585


title: acc, ctrl, rep7

description:
column number 13
BBBD12

value: bulk tissue

value: wildtype

value: ctrl (no light)


title: Total RNA-seq Hindlimb (Pbx1/Pbx2 mutant; rep. 2)


title: Ribo-seq MCMV 24hpi - Cycloheximide - Rep 1

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV, 24 h p.i.

value: MCMV

value: AATA


title: D11-B2-BRA-AD

value: lung adenocarcinoma

value: brain metastases


title: Ribo-seq MCMV 12hpi - Cycloheximide - Rep 1

value: MCMV, 12 h p.i.

tag: infection with

value: CCAC

value: Replicate 1


title: D10-I9-normal

source_name: normal lung

value: normal lung


title: 11H_M_2584


title: Ribo-seq MCMV 6hpi - Cycloheximide - Rep 1

value: MCMV, 6 h p.i.

tag: barcode

value: GGTC

value: Ribosome protected RNA fragments (29-30nt)

value: Cycloheximide


title: D09-I6-normal


title: Total RNA-seq Hindlimb (Pbx1/Pbx2 mutant; rep. 1)

value: embryonic hindlimb bud

value: gestational day e10.5

tag: replicate

value: Unstranded


title: 11H_M_2583


title: Ribo-seq MCMV 2hpi - Cycloheximide - Rep 1

value: Immortalized embryonic fibroblasts

value: MCMV, 2 h p.i.

value: TGGC

tag: molecule type


title: D08-I5-normal

tag: tissue


title: Total RNA-seq Hindlimb (Pbx1/Pbx2 ctrl; rep. 3)


title: 11H_M_2582


title: 11H_M_2581


title: Total RNA-seq Hindlimb (Pbx1/Pbx2 ctrl; rep. 2)


title: Ribo-seq Mock - Cycloheximide - Rep 1

value: Mock

value: GGCG


title: D07-I4-normal

value: lung adenocarcinoma


title: D06-I1-normal


title: Total RNA-seq Hindlimb (Pbx1/Pbx2 ctrl; rep. 1)


title: 4sU-seq Mock1 total B

description:
Purified nascent RNA following 1h of 4sU labeling was subjected to strand-specific RNA sequencing using random priming without rRNA depletion.
MCMV_polya.tar.gz
MCMV_introns.tar.gz

data_processing:
Bowtie2 2.3.0 was used to align all reads to ribosomal rRNA and Mycoplasma. Reads mapped to ribosomal rRNA and Mycoplasma were discarded.
STAR 2.5.3a was used to align the remaining reads to the mouse genome, Ensembl transcripts (v90), the MCMV genome (KY348373), and the MCMV transcripts (KY348373).
ContextMap 2.0 was used to identify poly(A) sites and introns as described in Whisnant A.W. et al, Nat. Commun (2020)
Assembly: GRCm38, KY348373
Supplementary files format and content: .bed files containing all poly(A) sites from each condition / time point. Tab separated files and Microsoft Excel files showing all introns.

growth_protocol: NIH-3T3 cells were cultured in DMEM supplements with 10% NCS and Pen-Strep, 100 IU/mL and 100µg/mL, respectively. Cells at passage 6 after thawing were infected at 80% confluency 24h after the last split.

extract_protocol:
Cells were lyzed using Trizol and total cellular RNA was isolated. 4sU labelled RNA was biotinylated using Biotin-HPDP followed by separation of new and old RNA using streptavidin-coated magnetic beads. Bead bound RNA was recovered via DTT treatment followed by RNA purification using Qiagen RNeasy MinElute columns.
Sequencing libraries were prepared for both total and newly transcribed RNA (4sU-RNA) as described in Rutkowski, A.J. et al, Nat. Commun (2015).

treatment_protocol: Cells were infected for 30 min with Smith strain MCMV at an MOI of 10 with centrifugal enhancement at 800g/30mins. Cell culture media was replaced 30 min later (infection time point t=0). Metabolic RNA labelling was performed by adding 200µM 4sU to the cell culture medium one hour prior to cell lysis.

value: Replicate 2

tag: molecule subtype

value: Purified nascent RNA


title: 4sU-seq MCMV 6hpi total B

tag: cell type

value: MCMV


title: Total RNA-seq Hindlimb (Hand2 mutant; rep. 3)

tag: genotype


title: 11H_M_2579


title: Total RNA-seq Hindlimb (Hand2 mutant; rep. 2)


title: 11H_M_2580


title: 11H_M_2578


title: D05-I9-LUAD

source_name: lung adenocarcinoma


title: 4sU-seq MCMV 48hpi total B

value: MCMV, 48 h p.i.


title: Total RNA-seq Hindlimb (Hand2 mutant; rep. 1)


title: 11H_M_2577

source_name: C57BL/6J Male P56 Mouse Brain


title: D04-I6-LUAD


title: 4sU-seq MCMV 24hpi total B

value: MCMV, 24 h p.i.


title: 4sU-seq MCMV 18hpi total B

value: MCMV, 18 h p.i.


title: Total RNA-seq Hindlimb (Hand2 ctrl; rep. 4)


title: D02-I4-LUAD


title: D03-I5-LUAD


title: 11H_M_2576


title: 4sU-seq MCMV 12hpi total B

value: MCMV, 12 h p.i.


title: D01-I1-LUAD


title: 11H_M_2575


title: Total RNA-seq Hindlimb (Hand2 ctrl; rep. 2)


title: 4sU-seq Mock1 total A

value: Replicate 1


title: 11H_M_2574


title: Total RNA-seq Hindlimb (Hand2 ctrl; rep. 1)

value: embryonic hindlimb bud


title: G3BP2 IgG control

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

description:
Human ESC G3BP2 CLIP-seq IgG control
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.

data_processing:
Reads were demuliplexed by using codes in the id of each reads by using the ShortRead package in BioConductor. Identical sequences were collapsed using the occurrenceFilter function in the ShortRead package.
3' adapter sequences were trimmed using the trimLRPatterns function in the ShortRead package. The 3' adapter sequences trimmed were sequences containing CCTGTGGTCGTAGCATCAGCTA.
The trimmed sequences were collapsed and converted to reverse complementary sequences.
CLIP-seq reads were sequentially mapped to rRNA, snRNA, snoRNA, tRNA and microRNA precursors sequences using Bowtie verions 1.12.7 with the following configurations -q –m 70 -n 2 -l 44 -5 1 -3 5 -a --best --strata -p 11 --sam --norc for noncoding RNAs. The remaining reads were aligned with the hg19 human genome  with the configuration -q –m 1 -n 0 -l 70 -5 1 -3 5 -a --best --strata -p 11 --sam  unique genomic sequences to generate bedGraph files.
Assembly: UCSC reference human genome hg19
Supplementary files format and content: bedGraph. Scores stand for CLIP-seq read coverage

growth_protocol: The H1 hESC cells were maintained on a mitotically inactivated mouse feeder (MEF) layer as follows. As a culture medium, DMEM/F12 supplemented with 20% Knockout Serum Replacement, 1% MEM non-essential amino acids, 1mM L-glutamine, 0.1mM β-mercaptoethanol and 4ng/ml basic FGF (Invitrogen) was used. Before analyses, hESCs were passaged three times without the feeder cells. For feeder-free culture, hESCs were dissociated with collagenase IV and plated on a Geltrex-coated plate with MEF-conditioned media supplemented with 50ng/ml basic FGF.

extract_protocol:
Two million cells were resuspended in 250 μl lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing EDTA-free protease inhibitor cocktail (Roche) and RNase inhibitor (Ambion) and briefly sonicated by using the Bioruptor.
The lysates were treated with 5 μl of Turbo DNase (Ambion) and 10 μl of 10 U/μl or 1 U/μl RNase I (Ambion) at 37°C for 3 min. Cellular debris was removed by centrifugation at 13,000 rpm for 15 min. Protein-RNA complexes were immunopurified with anti-L1TD1 (Sigma-Aldrich, HPA030064), anti-G3BP2 ( Bethyl, A302-040A ) or IgG antibody (Bethyl laboratories) bound to Protein A/G Dynabeads. Beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS) followed by two washes with PNK buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20). For dephosphorylation of 3’ ends, 1U of FastAP alkaline phosphatase (Fermentas) was added to the beads and incubated at 37°C for 20 min. After washing the beads twice with PNK buffer, protein-bound RNAs were ligated to a pre-adenylylated 3’ adaptor overnight at 16°C. Beads were washed twice with PNK buffer again and labeled with [γ- 32P] ATP for visualization. The labeled RNAs were separated by 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane, and excised from the membrane. The protein was degraded by proteinase K treatment, and RNA was recovered by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Protein-associated RNAs purified by IP or CLIP were ligated to a pre-adenylylated 3’ adaptor that contains a 2-nt adapter code for de-multiplexing and a 3-nt random sequence to minimize the loss of information after collapsing identical sequences. The RNA-adapter hybrids were converted into cDNAs with RT primer and SuperScript III reverse transcriptase (Invitrogen). The cDNAs were size-fractionated by electrophoresis on a 12% denaturing polyacrylamide gel and circularized by single-stranded DNA ligase (Epicentre). Circularized cDNAs were amplified with PCR primers, in which one of them contained a 6-nt primer code for de-multiplexing. PCR products were purified by agarose gel elution and subjected to next-generation sequencing.

treatment_protocol: For CLIP experiments H1 cells were irradiated with 300 mJ/cm2 of UVC light (254 nm) by using the CL-1000 ultraviolet crosslinker (UVP).

tag: cell line

value: Human embryonic stem cell

value: Wild type


title: 4sU-seq MCMV 6hpi total A

value: Immortalized embryonic fibroblasts

value: MCMV, 6 h p.i.


title: Pbx1 ChIP-seq Input DNA Replicate 2

data_processing:
Reads were aligned to the mm10 release of the mouse genome using Bowtie (PMID: 19261174) with parameters -v 2 -m 1.
Peak calling was performed using Model-Based Analysis for ChIP-seq (MACS) v1.4 (PMID: 18798982) with matched input DNA as control and parameters --gsize=mm --bw=150 --nomodel --shiftsize=100.
Genome_build: mm10
Supplementary_files_format_and_content: *_peaks.bed, list of peaks called with MACS

source_name: embryonic hindlimb bud, ChIP input

growth_protocol: Mice were maintained in animal facilties under standard conditions.

extract_protocol:
Embryonic hindlimb buds were isolated from E10.5 mouse embryos, obtained from timed matings of wild-type Swiss Webster mice and immediately crosslinked for 10 min in 1% formaldehyde (Electron Microscopy Sciences, #15710). The crosslinked material was sonicated to 200-500 bp fragments with a Diagenode Bioruptor. Each ChIP-seq assay was performed from pooling 60-80 embryonic hindlimbs, by overnight incubation with specific antibodies (5 µg) at 4°C followed by 30 min incubation with Dynabeads protein A (Invitrogen). After washing, IP and input DNA were de-crosslinked and purified using the MicroChIP DiaPure kit (Diagenode, #C03040001).
Libraries were constructed using the MicroPlex Library Preparation Kit v2 (Diagenode, C05010012). Libraries were normalized to 10 nM, pooled, and sequenced in an Illumina HiSeq 4000 to generate 50 base pair single-end reads.

value: Swiss Webster

value: gestational day e10.5

tag: antibody

value: none (input)


title: 4sU-seq MCMV 48hpi total A


title: 11H_M_2572

last: Ecker

tag: age

tag: strain


title: Pbx1 ChIP-seq Input DNA Replicate 1


title: 4sU-seq MCMV 24hpi total A


title: 11H_M_2573

tag: brain region


title: Hand2 ChIP-seq Input DNA Replicate 2

value: Hand2 3xFLAG


title: G3BP2 CLIP-seq replicate 2

description:
Human ESC G3BP2 CLIP-seq Low RNase replicate 1
Sequences from a U2AF1 IgG control CLIP library were combined to obtain sequence coverage.


title: G3BP2 CLIP-seq replicate 3

description:
Human ESC G3BP2 CLIP-seq High RNase replicate 2
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.


title: 11H_M_2571


title: 11H_M_2570


title: Hand2 ChIP-seq Input DNA Replicate 1


title: L1TD1 IgG control

description:
Human ESC L1TD1 CLIP-seq IgG control
Sequences from indepentent U2AF1 CLIP libraries were combined to obtain sequence coverage.


title: 4sU-seq MCMV 12hpi total A


title: Total RNA-seq Hindlimb (Hand2 ctrl; rep. 3)

value: Unstranded


title: H3K27me3 ChIP-seq Input DNA Replicate 1


title: 4sU-seq Mock1 new B

value: Mock

value: Replicate 2

value: Purified nascent RNA


title: L1TD1 CLIP-seq replicate 2

description:
Human ESC L1TD1 CLIP-seq Low RNase replicate 2
Sequences from indepentent U2AF1 CLIP libraried were combines to obtain sequence coverage.


title: H3K27me3 ChIP-seq Input DNA Replicate 2


title: L1TD1 CLIP-seq replicate 1

description:
Human ESC L1TD1 CLIP-seq Low RNase replicate 1
Sequences from indepentent U2AF1 CLIP libraries were combined to obtain sequence coverage.


title: H3K27ac ChIP-seq Input DNA Replicate 2


title: 11H_M_2567


title: 4sU-seq MCMV 6hpi new B

value: MCMV


title: G3BP2 CLIP-seq replicate 4

description:
Human ESC G3BP2 CLIP-seq Low RNase replicate 2
Sequences from indepentent ZRSR2 CLIP libraries were combined to obtain sequence coverage.


title: 4sU-seq MCMV 48hpi new B

value: MCMV, 48 h p.i.


title: 11H_M_2565


title: Pbx1 ChIP-seq Replicate 2

source_name: embryonic hindlimb bud, Pbx1 ChIP

value: Anti-PBX1; Cell Signaling, #4243S


title: High_salt_total_RNA

description: Human ESC mRNA-seq of total RNA

data_processing:
RNA-seq reads were sequentially mapped to the human genome GRCh37 using Hisat2 verions 2.1.0 with the following configurations -q -5 0 -3 0 --fr -p 11 -x  to generate bedGraph files.
Assembly: GRCh37
Supplementary files format and content: bedGraph. Scores stand for RNA-seq read coverage

extract_protocol:
For ribosome IP experiments, 24 hrs after the second transfection of siRNAs, 4 million cells were resuspended in 1 ml of IP buffer (50 mM Tris-HCl, pH7.5, 100 mM KCl, 12 mM MgCl2, 1 % NP40, 1 mM DTT, 100 unit/ml RNase inhibitor (Ambion), 1× protease inhibitor cocktail (Roche) and 100 𝛍g/ml cycloheximide). Cells were incubated on ice for 40 minutes with occasional inversion and centrifuged at 12,000g for 15 minutes at 4ºC. Fifty microliters of the cleared lysate were saved before combining the rest with 2.5 𝛍g of Y10b anti-5.8S RNA antibody immobilized on Protein G Dynabeads. The lysate-Dynabeads complex was rotated for 3 hrs at 4ºC, washed five times with high salt buffer (IP buffer with 300 mM KCl), and resuspended in Trizol for mRNA-seq analysis. For fractionation of RNA condensates, 2 million cells were resuspended in 250 𝛍l of fractionation buffer (50 mM Tris-HCl, pH7.6, 50 or 200 mM KCl, 5 mM MgCl2, 0.1 % NP40, 1 mM DTT, 100 unit/ml RNase inhibitor (NEB, #M0314), 1× protease inhibitor cocktail), incubated on ice for 10 minutes, and centrifuged at 2,000g for 2 minutes to remove nuclei. Cell lysates were transferred to new microfuge tubes and centrifuged again. After 40 microliters of the lysate were taken out for the total cytoplasmic lysate, 200 microliters of the lysate were centrifuged at 12,000g for 15 minutes. The upper fraction was saved as the supernatant. The pellet was washed twice with the fractionation buffer and resuspended in Trizol for RNA or 8M urea for protein analysis.
RNA integrity was confirmed by a bioanalyzer using an Agilent RNA 6000 Pico Kit (Agilent, Santa Clara, CA). The isolated total RNA was processed for preparing mRNA sequencing library using TruSeq stranded mRNA sample preparation kit (illumina, San Diego, CA) according to manufacturer’s instruction. Simply, mRNAs were isolated from 400 ng total RNA by RNA purification bead using polyA capture, and followed by enzyme shearing. After first and second strand cDNA synthesis, A-tailing and end repair were performed for ligation of proprietary primers that incorporate unique sequencing adaptors with index for tracking illumina reads from multiplexed samples run on a single sequencing lane. For each library, an insert size of approximately 200 bp was confirmed by a bioanalyzer using an Agilent DNA  Kit (Agilent, Santa Clara, CA) and quantification of library was measured by real-time PCR using CFX96 real time system (BioRad, Hercules, CA). All the samples were sequenced on Illumina NextSeq 500 Sequencer with 75-bp Paired end High Output Kit. The raw image data was transformed by base-calling into sequence data and stored in FASTQ format.

treatment_protocol: For ribosome IP experiments, 4 million cells were transfected with siRNAs.

tag: treatment

value: High salt total RNA


title: 4sU-seq MCMV 4hpi new B

value: MCMV, 4 h p.i.


title: 4sU-seq MCMV 18hpi total A

value: MCMV, 18 h p.i.

value: Replicate 1


title: H3K27ac ChIP-seq Input DNA Replicate 1

value: embryonic hindlimb bud

tag: developmental stage


title: RibosomeIP_siL1TD1

description: Human ESC Ribosome IP siL1TD1 mRNA-seq

value: Human embryonic stem cell

value: Wild type


title: 4sU-seq MCMV 24hpi new B

value: Immortalized embryonic fibroblasts

value: MCMV, 24 h p.i.


title: 11H_M_2566


title: G3BP2 CLIP-seq replicate 1

description:
Human ESC G3BP2 CLIP-seq high RNase replicate 1
Sequences from indepentent U2AF1 CLIP libraries were combined to obtain sequence coverage.


title: High_salt_precipitated_RNA

description: Human ESC mRNA-seq of condensates in a high-salt buffer

value: High salt precipitated RNA


title: 11H_M_2569


title: 11H_M_2563


title: Hand2 ChIP-seq Replicate 2

source_name: embryonic hindlimb bud, Hand2 ChIP

value: Hand2 3xFLAG

value: gestational day e10.5

value: M2 anti-FLAG antibody (Sigma F1804)


title: 4sU-seq MCMV 18hpi new B

value: Replicate 2

value: Purified nascent RNA


title: 4sU-seq Mock2 new B

value: Mock


title: 11H_M_2568


title: RibosomeIP_Input_siL1TD1

description: Human ESC Ribosome IP siL1TD1 input mRNA-seq


title: 11H_M_2562


title: Hand2 ChIP-seq Replicate 1


title: 4sU-seq MCMV 2hpi new B

value: MCMV, 2 h p.i.

value: MCMV


title: 11H_M_2561


title: RibosomeIP_siControl

description: Human ESC Ribosome IP siControl mRNA-seq

value: scrambled siRNA


title: 4sU-seq MCMV 12hpi new B

value: MCMV, 12 h p.i.


title: RibosomeIP_Input_siControl

description: Human ESC Ribosome IP siControl input mRNA-seq


title: Low_salt_precipitated_RNA

description: Human ESC mRNA-seq of condensates in a low-salt buffer

value: Low salt precipitated RNA