title: CEMBA180910_5J_3_CEMBA180910_5J_4_D4_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D5_ad006

status: Public on Sep 08 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
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
Genome_build: 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

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

value: CP

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D4_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D4_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D4_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D7_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D3_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D2_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D2_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D12_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D2_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D12_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D12_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D12_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D12_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D11_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D11_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D11_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D11_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D11_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D12_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C9_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C9_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D11_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C9_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C9_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D10_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_D1_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C9_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C6_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C6_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C6_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C6_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C8_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C4_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C4_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C5_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C3_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C4_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C4_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C7_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C3_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C3_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C3_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C3_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C3_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C6_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C2_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C10_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C10_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C10_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C10_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C10_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C10_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C1_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B9_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B9_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B9_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B9_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C11_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B9_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B8_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B9_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B8_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B8_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B8_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B7_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B7_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B7_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B7_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B6_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B7_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B5_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B6_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B6_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B5_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B5_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B5_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B5_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B5_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_C12_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B7_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B6_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B6_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B3_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad006


title: SpeciesMix2_ATAC

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: tagmented gDNA

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38-mm10 reference genome
For ADT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

organism:
Homo sapiens
Mus musculus

source_name: Cell lines

extract_protocol:
Samples were stained with hashing and surface marker antibodies, fixed with 1% PFA and then extracted using the 10x Genomics OMNI protocol.
ATAC libraries were constructed according to the 10x Genomics scATAC-seq v1 protocol. Antibody tags were captured via the bridge oligo spiked-in the barcoding reaction and amplfication using tag-specific handles was performed using as input fragments before or after SPRI purification as indicated.

treatment_protocol: HEK-293 and NIH-3T3 cells were stained with hCD29 and mCD29, washed, fixed and lysed using the OMNI lysis buffer

tag: cell line

value: mixture of HEK-293 and NIH-3T3

tag: target molecule

value: Accessible chromatin

tag: ab tags

tag: lysis buffer

value: OMNI

tag: tag library input

value: post-SPRI


title: SpeciesMix2_ADT

description: antibody oligos

value: Cell Surface Markers

value: 15 bases tag (2 tags total)


title: SpeciesMix1_ATAC

description: tagmented gDNA

value: pre-SPRI


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B2_ad012


title: Human_BoneMarrow_HTO

description: antibody oligos

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
We further provide fragment counts for an hg19 alignment for community use.
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38 / hg19
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Samples were stained with hashing and surface marker antibodies, fixed with 1% PFA and then extracted using the mtscATAC-seq
ATAC libraries were constructed according to the 10x Genomics scATAC-seq v1 protocol while antibody tags were captured via the bridge oligo spiked-in the barcoding reaction and amplfied using tag-specific handles.

treatment_protocol: Thawed cryopreserved bone marrow cells were stained with 6 TSA hashing antibodies and the BM antibody panel (242 antibodies), washed, fixed and lysed using the LLL lysis buffer

tag: tissue

value: Bone Marrow

value: Cell Surface Markers for Hashing

value: 15 bases tag (6 tags total)

value: LLL


title: SpeciesMix1_ADT

description: antibody oligos


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B10_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B10_ad012


title: Perturb_CD4_stim_HT2

description: antibody oligos

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
gRNA-based KOs were assigned based on a modified version of HTO Demux.
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

source_name: T-cells from peripheral blood mononuclear cells

growth_protocol: Cells were stimulated for 72 hours, followed by 4 days resting and then electroporation with Cas9 protein. Samples were treated with distinct gRNAs based on the overall design. Cells were further expanded an additional 7 days

extract_protocol:
Samples were stained with hashing antibodies for multiplexing gRNAs and surface marker antibodies, fixed with 1% PFA and then extracted using the 10x protocol (Omni-ATAC)
ATAC libraries were constructed according to the 10x Genomics scATAC-seq v1.1 protocol while antibody tags were captured via the bridge oligo spiked-in the barcoding reaction and amplfied using tag-specific handles.

treatment_protocol: Cells were re-stimulated for 72 hours and then enriched for live cells by cell sorting

tag: donor #

value: Three distinct biological donors

tag: ab treatment

value: CD298/Beta2 microglobulin hash antibodies corresponding to CRISPR gRNA

tag: elution

value: SPRI supernatent

tag: knockdown

value: mixed sample (non-demultiplexed)


title: Human_BoneMarrow_ADT

description: antibody oligos

value: 15 bases tag (242 tags total)


title: Perturb_CD4_stim_HT1

description: antibody oligos

value: silane elute


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B10_ad002

value: CP

value: male


title: Human_BoneMarrow_ATAC

description: tagmented gDNA

value: Accessible chromatin


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B10_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B4_ad001


title: Perturb_CD4_stim_ATAC

description: antibody oligos


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B12_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad008


title: Perturb_CD4_stim_AD2

description: antibody oligos

value: Selected cell surface markers


title: Perturb_CD4_stim_AD1

description: tagmented gDNA


title: Intra_TSB

description: antibody oligos

data_processing:
Library strategy: ASAP-seq
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library

source_name: Peripheral blood mononuclear cells

extract_protocol:
Samples were stained with hashing and surface marker antibodies, fixed with 1% PFA and then extracted using the mtscATAC-seq or Omni ATAC as indicated in different lysis conditions
ATAC libraries were constructed according to the 10x Genomics scATAC-seq v1 protocol while antibody tags were captured via the bridge oligo spiked-in the barcoding reaction and amplfied using tag-specific handles.

treatment_protocol: Thawed cryopreserved PBMCs were stained with either TSA TBNK panel only (Broad samples) or with 1:1 mix of TSA:TSB TBNK panel (AvsB samples) or with TSA extracellular TBNK followed by TSB intracellular staining, using the indicated lysis conditions.

value: Intracellular Markers

value: 15 bases tag (3 tags total)

value: OMNI


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad010


title: Intra_TSA

description: antibody oligos

value: Cell Surface Markers

value: 15 bases tag (8 tags total)


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B11_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad006


title: Intra_ATAC

description: tagmented gDNA

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
For ADT and HTO count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for the protein count data including the ATAC singlecell QC metrics; barcoded accessible chromatin fragments per ATAC library


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A9_ad002


title: Broad_LibB_ATAC

description: tagmented gDNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad001


title: Broad_LibC_ATAC

description: tagmented gDNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad002


title: Broad_LibC_HTO

description: antibody oligos

value: Cell Surface Markers for Hashing

value: 15 bases tag (4 tags total)


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A9_ad012


title: AvsB_TSB_LLL

description: antibody oligos

value: LLL


title: AvsB_TSB_OMNI

description: antibody oligos


title: Broad_LibA_ATAC

description: tagmented gDNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A9_ad008


title: Broad_LibB_ADT

description: antibody oligos


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A9_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_B1_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A8_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A8_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A8_ad012


title: AvsB_TSA_OMNI

description: antibody oligos


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A8_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A8_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A8_ad001


title: AvsB_TSA_LLL

description: antibody oligos


title: AvsB_ATAC_OMNI

description: tagmented gDNA


title: PFF [PEF-2_S5]

city: Seoul

first: Chang-Kyu

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

library_source: transcriptomic

data_processing:
RNA sequencing was performed using HiSeq2500 (Illumina). Low-quality reads were filtered out with following criteria: lack adaptor sequences, < 17 base pairs, : > 90 % of reads survived. Adaptors were trimmed out using Cutadapt (v1.10).
Filtered reads were aligned to pig genome using Bowtie (v1.1.1) and Samtools (v1.2): 70.32 - 92.19 % reads were mapped: Ensembl 72 (S_scrofa). Known and novel miRNAs were identified using miRDeep2 (v2.0.0.7). Reads were quantified using HTseq (v0.6.1p1).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: locus and raw counts of sequencing reads

molecule: total RNA

organism: Sus scrofa

source_name: PFF

growth_protocol: Porcine embryos were produced by the parthenogenetic activation method. The embryos were cultured in PZM3 medium with 5% CO2 and 5% O2 at 37°C until sampling on day 7. Fetal bovine serum was added onto the medium with 10% concentration on day 4. Pig embryonic stem-like cells (ES-like cells) were cultured with ES-like cell media consisted of 1:1 mixture of Dulbecco’s modified Eagle’s medium (DMEM) and Ham’s F10 media containing 15% fetal bovine serum (FBS; collected and processed in the USA), 2 mM glutamax, 0.1 mM β-mercaptoethanol, 1x MEM nonessential amino acids, 1x antibiotic–antimycotic (all from Gibco, USA), 40 ng/ml human recombinant stem cell factor (hrSCF; R&D Systems, USA) and 20 ng/ml human recombinant basic fibroblast growth factor (hrbFGF; R&D Systems). ES-like cell colonies were cultured in hanging-drops without cytokines to form embryoid bodies (EBs). Pig fetal fibroblasts (PFFs) were cultured in DMEM (Welgene, Korea) supplemented with 10% fetal bovine serum (FBS; collected and processed in the United States; Genedepot, TX, USA), 1× glutamax (Gibco), 0.1 mM ß-mercaptoethanol (Gibco), and 1× antibiotic/antimycotic (Gibco).

extract_protocol:
MicroRNAs from all samples were extracted using mirVANA miRNA Isolation Kit following user guide
NEXTFLEX® Small RNA-Seq Kit v3 for Illumina® Platforms was used to prepare RNA library

tag: sample/tissue type

value: Cell line

tag: cell type

value: Pig fetal fibroblasts

tag: molecule subtype

value: microRNA


title: PEB [PES-EB_S4]

source_name: PEB

value: Embryoid body

value: Pig embryoid body from ES-like cells


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad006

tag: brain region

value: CP


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad007

tag: Sex

value: male


title: PA-BL-2 [BL355M_S2]

source_name: PA-BL

value: Pig embryo

value: Day 7 PA blastocysts


title: Pig ES-like cell [PES_S3]

source_name: Pig ES-like cell

value: Embryonic stem cell-like cells


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad004

tag: age


title: PA-BL-1 [BL126_S1]


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad008

tag: strain


title: ChIPseq PBX in EB-Day4[D0+RA+SAG][D2+Dox(iFlag.Hoxc10)] replicate 1

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using Picard (v 2.8.2)
Alignment: ChIP-seq reads were aligned to the mm10 genome using Bowtie (v1.0.1) (Langmead, Trapnell, Pop, & Salzberg, 2009), using options “-q --best --strata -m 1 --chunkmbs 1024”.
Binding Event Detection: Genome-wide TF binding events.txt were called in each condition using MultiGPS (v0.74) (Mahony et al., 2014). EdgeR (v3.22.5) was used within the MultiGPS framework to test whether genomic sites were differentially bound by TFs (Robinson, McCarthy, & Smyth, 2010). A genomic site was defined as shared by TFs if significant binding events.txt were called in both TF ChIP-seq experiments (q-value < 0.001), and the TFs did not display differential read enrichment at that site as estimated by EdgeR (q-value > 0.01). A binding event was defined as “TF1>TF2” if a MultiGPS peak was called in TF1 ChIP-seq (q-value < 0.001), TF1 exhibited a greater log fold-change with respect to the input ChIP-seq than TF2, and TF1 and TF2 were significantly differentially bound as defined by EdgeR (q-value < 0.01). A similar strategy was applied to perform multi-way ChIP-seq comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

source_name: ES-derived embryoid bodies+4D RA+SAG with induced transcription factors

growth_protocol: mESC lines were cultured in 2-inhibitors based medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (Millipore), 3μM CHIR (BioVision) and 1 μM PD0325901 (Sigma)) on 0.1% gelatin (Millipore) coated plates at 37 °C, 8% CO2.

extract_protocol:
Cells were collected 24h and 48h after Doxycycline (Dox) treatment. Crosslinking was performed at room temperature in 1mM DSG (ProteoChem) for 15min, followed by the addition of 1% FA (vol/vol) for an additional 15min. After quenching with Glycine, cells were divided into ~25-30x106 aliquots, pelleted by centrifugation and frozen at -80°C. After thawing cells on ice, lysis was performed in 5mL of 50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1× protease inhibitors (Roche, 11697498001) for 10 min at 4 °C. Cells were centrifuged for 5min, resuspended in 5mL of 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with 1× protease inhibitors, and incubated for 10 min at 4 °C on a rotating platform. Cells were centrifuged for 5min and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1× protease inhibitors). Sonication was performed by splitting each sample to 2 Bioruptor tubes with sonication beads and using the Bioruptor Pico (Diagenode) for 18 cycles of 30 sec on and 30 sec off into an average size of approximately 200 bp. Immunoprecipitation was performed for 16h at 4 °C on a rotating platform by incubating with Dynabeads protein-G (Thermo Fisher Scientific) conjugated with 5 µg of one of the following antibodies: mouse monoclonal antibody to Flag (Sigma, F1804) or rabbit polyclonal antibody to HA (Abcam, ab9110).
lllumina DNA sequencing libraries were prepared with one third of the ChIP sample or a 1:100 dilution of the input sample in water. Library preparation was performed by end repair, A-tailing and ligating Illumina-compatible Bioo Scientific multiplexed adapters. Unligated adapters were removed using Agencourt AmpureXP beads (Beckman Coulter). Amplification was performed by PCR with Phusion polymerase (New England Biolabs) and TruSeq primers (Sigma). Libraries were gel purified (Qiagen) between 250 and 550bp in size. Final quantification of the library was performed using the KAPA library amplification kit on the Roche Lightcycler 480 before pooling.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For ChIP-seq experiments, 3-3.5x10^6 mESCs were plated in 245mm x 245mm square dishes (Corning).

tag: strain genotype/variation

tag: treatment

value: EB + 4 Days RA + SAG, D2+48hours Dox

value: Embryoid Bodies

tag: chip target

value: PBX

tag: chip antibody

value: sc-28313 (SantaCruz)


title: Dexamethasone rep 2

city: Jupiter

first: Jerome

last: Nwachukwu

state: Florida

address: 130 Scripps Way

department: Department of Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

data_processing:
Primary data analysis including base calling and quality scoring was performed in real-time on the NextSeq 500 platform.
Reads were aligned to the mm9 assembly using Tophat v2.0.13
Sorting and indexing was performed using SAMtools v1.1
The number of read counts were quantified using HTSeq-count v0.6.1
Differential expression analysis was performed using DESeq2 v1.18.1
Genome_build: mm9
Supplementary_files_format_and_content: A matrix table containing the raw counts of sequencing reads for each gene

molecule: nuclear RNA

source_name: C2C12 myotubes

extract_protocol:
Nuclei were isolated, washed, and lysed with a 10% NP40 buffer and centrifuged. The pellet was washed 2x with TRIzol™ reagent (Invitrogen) to remove unbound RNA. The chromatin pellet was then dissolved in Trizol at 65°C and RNA was isolated using standard protocols  for Qiashredder and RNeasy column purification). Sequencing libraries were constructed using using the TruSeq stranded total RNA kit (Illumina).
Sequencing libraries were constructed using standard Illumina TruSeq Stranded mRNA library prep protocol

tag: cell line

value: female

tag: developmental stage

value: myotubes

value: Skeletal muscle

tag: compound

value: 1 uM Dexamethasone


title: Vehicle rep 2

tag: tissue

value: Vehicle


title: ChIPseq PBX in EB-Day4[D0+RA+SAG][D2+Dox(iFlag.Hoxc9)] replicate 1


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A6_ad010


title: FLOX_SD_03

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: Total RNA

data_processing:
Demultiplexed FASTQ files received from NGS core.
FASTQ files were checked for quality and trimmed.
Trimmed FASTQ files were aligned to reference genome.
Uniquely mapped reads were exxtracted and counted per gene.
Differential gene expression and network analysis was performed.
Genome_build: MM10

source_name: frontal cortex

extract_protocol: Total RNA was extracted with Trizol reagent and purified with RNeasy kit according to manufactures' protocols.

tag: genotype

tag: background

value: M

value: Adult

tag: sleep state

value: sleep deprived (6 hrs)


title: Vehicle rep 1


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad010

value: CP


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad012

value: male


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad002


title: FLOX_SD_02

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A6_ad012


title: AvsB_ATAC_LLL

description: tagmented gDNA

tag: target molecule

value: Accessible chromatin

tag: ab tags

tag: lysis buffer

value: LLL


title: Dexamethasone rep 1

tag: Sex


title: FLOX_SD_01

description: Total RNA

tag: age


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A6_ad001

tag: brain region

tag: strain


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A5_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A7_ad001


title: FLOX_CS_03

description: Total RNA

value: sleep ad libitum


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A5_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A5_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A5_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A5_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A5_ad001


title: FLOX_CS_02

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A4_ad007


title: FLOX_CS_01

description: Total RNA


title: FLOX_CS_04

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A4_ad012


title: CKO_CS_07

description: Total RNA


title: CKO_SD_06

description: Total RNA


title: CKO_CS_05

description: Total RNA


title: CKO_SD_07

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A3_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A4_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A4_ad002


title: CKO_SD_05

description: Total RNA


title: CKO_CS_08

description: Total RNA


title: WT_RS_06

description: Total RNA

value: Wild-type (C57BL/6J)

value: recovery sleep (2 hrs)


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A3_ad007


title: WT_RS_12

description: Total RNA


title: WT_RS_05

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad010


title: WT_RS_03

description: Total RNA


title: WT_SD_06

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad008


title: WT_SD_03

description: Total RNA


title: WT_RS_02

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A3_ad002


title: WT_SD_09

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad004


title: WT_SD_08

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A3_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad012


title: WT_SD_04

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A3_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A12_ad004


title: WT_RS_04

description: Total RNA


title: WT_CS_06

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A12_ad010


title: WT_CS_05

description: Total RNA


title: WT_SD_01

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A12_ad006


title: WT_SD_02

description: Total RNA


title: WT_CS_04

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A12_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A2_ad002


title: WT_CS_03

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A12_ad002


title: WT_RS_01

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A12_ad008


title: WT_CS_02

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A11_ad012


title: WT_CS_01

description: Total RNA


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A11_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A11_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A11_ad010


title: 2017_563h: C3-PAP-GFP technical replicate 8

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: PAP, GFP, Animal C3, technical replicate 8

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
The analyses were performed using the Eoulsan pipeline, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, adapters were removed using Trim Galore 0.4.1, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the mouse genome from Ensembl version 84 using STAR (version 2.5.2b). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, mouse GTF genome annotation version 84 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3.
Genome_build: mm10 (Ensembl 84)
Supplementary_files_format_and_content: tab-delimited text files include gene counting for each sample

source_name: dorsal hippocampus

extract_protocol:
Polysomes were extracted using our recently published TRAP protocol (Boulay AC et al., Methods Mol Biol. 2019). In order to avoid nonspecific binding of the mRNAs to the beads or to IgG, and in contrast to the initial TRAP protocol (Heiman M et al., Nat Protoc. 2014), the cytosolic extracts were pre-cleaned more extensively prior to immunoprecipitation. Lysates were first placed on an antibody-free pre-cleaning column and then on a column with bound nonspecific mouse IgGs. Nonspecific sites on the immunoprecipitation column were blocked with yeast tRNA and BSA. Polysomal mRNAs were purified using the RNeasy Lipid tissue kit (Qiagen).
10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards an average of 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina)

value: Tg(Aldh1l1-eGFP/Rpl10a) JD130Htz (MGI:5496674) (Aldhl1:L10a-eGFP)

value: dorsal hippocampus

tag: cell part

value: PAP

tag: antiboby

value: GFP

tag: animal id

value: Animal C3


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A11_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad004


title: 2017_563f: C3-PAP-GFP technical replicate 6

description: PAP, GFP, Animal C3, technical replicate 6


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A11_ad002


title: 2017_563e: C3-PAP-GFP technical replicate 5

description: PAP, GFP, Animal C3, technical replicate 5


title: 2017_563g: C3-PAP-GFP technical replicate 7

description: PAP, GFP, Animal C3, technical replicate 7


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad006


title: 2017_563d: C3-PAP-GFP technical replicate 4

description: PAP, GFP, Animal C3, technical replicate 4


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad008


title: Pat1_cHCV_P1_7

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

molecule: polyA RNA

source_name: Cryopreserved PBMCs, Department of Medicine II of the University Hospital Freiburg, Germany

extract_protocol:
PBMCs from EDTA anticoagulated patient blood were isolated by density gradient centrifugation using Pancoll (Pan-Biotech, Germany). Magnetic bead-based enrichment of antigen-specific CD8 T cells was further performed. For magnetic bead-based enrichment of HCV-specific CD8+ T cells PBMCs were incubated with peptide-loaded HLA- tetramers coupled to phycoerythrin (PE). Subsequent enrichment was performed with anti-PE beads using the MACS technology (Miltenyi Biotec, Germany) according to the manufacturer’s protocol. Enriched HCV-specific CD8+ T cells were used for multiparametric flow cytometry and transcriptome analysis. Epitope-specific HLA tetramers were generated by conjugation of biotinylated peptide-MHC class I monomers with PE-conjugated streptavidin at a HLA:Strepatividin molar ratio of 5:1. The following peptide-loaded HLA tetramers were used: NS31073(CINGVCWTV)/HLA-A*02:01; NS31406(KLVALGINAV/KLSGLGLNAV)/HLA-A*02:01; NS52594(ALYDVVTKL)/HLA-A*02:01; and NS5B2841(ARMILMTHF)/HLA-B*27:05.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: disease state

value: chronic HCV infection

value: Peripheral Blood

tag: cell type

value: HCV-specific CD8+ T cells


title: Pat1_cHCV_P1_8


title: 2017_563c: C3-PAP-GFP technical replicate 3

description: PAP, GFP, Animal C3, technical replicate 3


title: Pat1_cHCV_P1_6


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad010


title: R50TD: Patient #50 rectal tumor stem cells-VitaminD

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

country: Spain

institute: IIB

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Sequencing reads were aligned to the transcriptome with TopHat2
TopHat was provided with known gene annotations and other transcript data obtained from Gencode (Version 26 - Ensembl 75) basic gene set for the GRCh37/hg19 human genome assembly
Gene expression level was calculated from TopHat alignments as the number of reads per gene computed using HTSeq using default settings and gene features as defined in the GRCh37.75 release of the human genome.
Differential gene expression analysis was performed with the Bioconductor DEseq2 package for the R statistical Software
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited files and excell files containing cpm, and statistics

source_name: stem cell enriched organoid primary culture

growth_protocol: Cells were seeded in Matrigel and grown according to Clevers el all 2011 For both healthy and tumor tissue

extract_protocol:
Macherey-Nagel RNA extraction Kit was used in combination with TRIZOL. Both large and small RNA was extracted.
1 µg of total RNA samples was used. Average sample RNA Integrity Number was 9.7 (range 8.1 - 10) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: Cells were treated with 1,25(OH)2D3 [100nM] or vehicle (EtOH) for 96 hours. The treatment was started 48 hours after passage and 1,25(OH)2D3 was renewed every 48 houres.

value: rectal tumor

tag: gender

value: Male

tag: tnm

tag: treatment

tag: tumor site

value: Upper rectum


title: 2017_563a: C3-PAP-GFP technical replicate 1

description: PAP, GFP, Animal C3, technical replicate 1

tag: tissue


title: Pat1_cHCV_P1_5


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A10_ad001

value: CP

value: male


title: 2017_563b: C3-PAP-GFP technical replicate 2

description: PAP, GFP, Animal C3, technical replicate 2


title: R50TC: Patient #50 rectal tumor stem cells-Control

value: Vehicle


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A1_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A1_ad006


title: 2017_561h: C3-Astro-GFP technical replicate 8

description: Full Astrocytes, GFP, Animal C3, technical replicate 8

value: Full Astrocytes


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A1_ad001


title: 2017_561g: C3-Astro-GFP technical replicate 7

description: Full Astrocytes, GFP, Animal C3, technical replicate 7


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A1_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H9_ad002


title: R49TC: Patient #49 rectal tumor stem cells-Control

value: Female


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A1_ad007


title: 2017_561f: C3-Astro-GFP technical replicate 6

description: Full Astrocytes, GFP, Animal C3, technical replicate 6


title: R48TD: Patient #48 rectal tumor stem cells-VitaminD

value: Medial rectum


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H9_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H8_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H9_ad006


title: R47TD: Patient #47 rectal tumor stem cells-VitaminD

value: Lower Rectum


title: 2017_561e: C3-Astro-GFP technical replicate 5

description: Full Astrocytes, GFP, Animal C3, technical replicate 5

value: Tg(Aldh1l1-eGFP/Rpl10a) JD130Htz (MGI:5496674) (Aldhl1:L10a-eGFP)

value: dorsal hippocampus


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H8_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_A1_ad002


title: 2017_561b: C3-Astro-GFP technical replicate 2

description: Full Astrocytes, GFP, Animal C3, technical replicate 2

value: GFP


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H7_ad002


title: R49TD: Patient #49 rectal tumor stem cells-VitaminD


title: 2017_561c: C3-Astro-GFP technical replicate 3

description: Full Astrocytes, GFP, Animal C3, technical replicate 3

value: Animal C3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H7_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H7_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H9_ad007


title: 2017_561a: C3-Astro-GFP technical replicate 1

description: Full Astrocytes, GFP, Animal C3, technical replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H6_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H6_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H5_ad001


title: R46TC: Patient #46 rectal tumor stem cells-Control


title: R45RD: Patient #45 rectum stem cells-Vitamin D

value: rectum


title: R48TC: Patient #48 rectal tumor stem cells-Control


title: 2017_561d: C3-Astro-GFP technical replicate 4

description: Full Astrocytes, GFP, Animal C3, technical replicate 4


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H8_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H5_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H5_ad004


title: R46TD: Patient #46 rectal tumor stem cells-VitaminD


title: 2017_555f: C2-PAP-GFP technical replicate 6

description: PAP, GFP, Animal C2, technical replicate 6

value: PAP

value: Animal C2


title: R47TC: Patient #47 rectal tumor stem cells-Control

value: rectal tumor


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H5_ad002


title: R45CD: Patient #45 colon stem cells-VitaminD

value: colon

value: Male


title: R45RC: Patient #45 rectum stem cells-Control


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H7_ad004

value: CP


title: 2017_555e: C2-PAP-GFP technical replicate 5

description: PAP, GFP, Animal C2, technical replicate 5


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H4_ad004

value: male


title: R45CC: Patient #45 colon stem cells-Control

value: Vehicle


title: 2017_555d: C2-PAP-GFP technical replicate 4

description: PAP, GFP, Animal C2, technical replicate 4


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H4_ad001


title: R44TD: Patient #44 rectal tumor stem cells-Vitamin D


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H4_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H4_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H3_ad006


title: 2017_555h: C2-PAP-GFP technical replicate 8

description: PAP, GFP, Animal C2, technical replicate 8


title: 2017_555c: C2-PAP-GFP technical replicate 3

description: PAP, GFP, Animal C2, technical replicate 3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H4_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H3_ad001


title: 2017_555g: C2-PAP-GFP technical replicate 7

description: PAP, GFP, Animal C2, technical replicate 7


title: 2017_555b: C2-PAP-GFP technical replicate 2

description: PAP, GFP, Animal C2, technical replicate 2


title: R44RD: Patient #44 rectum stem cells-Vitamin D


title: R44TC: Patient #44 rectal tumor stem cells-Control


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H3_ad004


title: 2017_555a: C2-PAP-GFP technical replicate 1

description: PAP, GFP, Animal C2, technical replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H3_ad002


title: R44RC: Patient #44 rectum stem cells-Control


title: 2017_553h: C2-Astro-GFP technical replicate 8

description: Full Astrocytes, GFP, Animal C2, technical replicate 8

value: Full Astrocytes


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H5_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H2_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H2_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H2_ad002


title: R44CC: Patient #44 colon stem cells-Control


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H12_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H2_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H12_ad008


title: 2017_553g: C2-Astro-GFP technical replicate 7

description: Full Astrocytes, GFP, Animal C2, technical replicate 7


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H12_ad002


title: 2017_553e: C2-Astro-GFP technical replicate 5

description: Full Astrocytes, GFP, Animal C2, technical replicate 5


title: 2017_553f: C2-Astro-GFP technical replicate 6

description: Full Astrocytes, GFP, Animal C2, technical replicate 6


title: R43RD: Patient #43 rectum stem cells-Vitamin D

value: Female


title: R43RC: Patient #43 rectum stem cells-Control


title: R43CD: Patient #43 colon stem cells-VitaminD


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H12_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H12_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H11_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H12_ad007


title: 2017_553c: C2-Astro-GFP technical replicate 3

description: Full Astrocytes, GFP, Animal C2, technical replicate 3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H11_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H11_ad012


title: R43CC: Patient #43 colon stem cells-Control


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H11_ad002


title: 2017_553b: C2-Astro-GFP technical replicate 2

description: Full Astrocytes, GFP, Animal C2, technical replicate 2


title: R42RD: Patient #42 rectum stem cells-Vitamin D


title: 2017_553a: C2-Astro-GFP technical replicate 1

description: Full Astrocytes, GFP, Animal C2, technical replicate 1


title: R42CD: Patient #42 colon stem cells-VitaminD


title: R44CD: Patient #44 colon stem cells-VitaminD


title: R42RC: Patient #42 rectum stem cells-Control


title: 2017_547h: C1-PAP-GFP technical replicate 8

description: PAP, GFP, Animal C1, technical replicate 8

value: Animal C1


title: 2017_547g: C1-PAP-GFP technical replicate 7

description: PAP, GFP, Animal C1, technical replicate 7


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H10_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H10_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H10_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H10_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H1_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H1_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H8_ad001


title: 2017_553d: C2-Astro-GFP technical replicate 4

description: Full Astrocytes, GFP, Animal C2, technical replicate 4


title: R42CC: Patient #42 colon stem cells-Control


title: 2017_547f: C1-PAP-GFP technical replicate 6

description: PAP, GFP, Animal C1, technical replicate 6


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H1_ad002


title: R41RD: Patient #41 rectum stem cells-Vitamin D


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H1_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H1_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G9_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_H10_ad006


title: R41RC: Patient #41 rectum stem cells-Control


title: 2017_547e: C1-PAP-GFP technical replicate 5

description: PAP, GFP, Animal C1, technical replicate 5


title: 2017_547d: C1-PAP-GFP technical replicate 4

description: PAP, GFP, Animal C1, technical replicate 4


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G9_ad002


title: R41CD: Patient #41 colon stem cells-VitaminD


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G8_ad006


title: 2017_547c: C1-PAP-GFP technical replicate 3

description: PAP, GFP, Animal C1, technical replicate 3


title: R41CC: Patient #41 colon stem cells-Control


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G8_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G8_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G8_ad002


title: R40RD: Patient #40 rectum stem cells-Vitamin D


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G7_ad002


title: 2017_547a: C1-PAP-GFP technical replicate 1

description: PAP, GFP, Animal C1, technical replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G7_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G7_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G7_ad004


title: R40CD: Patient #40 colon stem cells-VitaminD


title: 2017_545h: C1-Astro-GFP technical replicate 8

description: Full Astrocytes, GFP, Animal C1, technical replicate 8


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G6_ad008


title: 2017_545f: C1-Astro-GFP technical replicate 6

description: Full Astrocytes, GFP, Animal C1, technical replicate 6


title: 2017_545g: C1-Astro-GFP technical replicate 7

description: Full Astrocytes, GFP, Animal C1, technical replicate 7


title: R40CC: Patient #40 colon stem cells-Control


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G6_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G5_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G5_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G9_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G4_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G5_ad001


title: 2017_545e: C1-Astro-GFP technical replicate 5

description: Full Astrocytes, GFP, Animal C1, technical replicate 5


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G5_ad006


title: SUZ12_SU-DIPG-XIII_(20180425_JS_HsDmSc_0330_JS256)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&RUN for SUZ12 in 1M SU-DIPG-XIII cells

data_processing:
Library strategy:  CUT&RUN
Genome_build: UCSC hg19
Genome_build: Masked UCSC dm6
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used bowtie 2.2.5 with options "--local --very-sensitive-local --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to masked UCSC dm6. 3. We extracted properly paired reads from the marked alignments to both genomes. 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz).

source_name: SU-DIPG-XIII cells; anti-SUZ12 abcam ab12073

tag: cell line

value: SU-DIPG-XIII cells

tag: antibody

value: anti-SUZ12 abcam ab12073


title: 2017_545d: C1-Astro-GFP technical replicate 4

description: Full Astrocytes, GFP, Animal C1, technical replicate 4

value: Tg(Aldh1l1-eGFP/Rpl10a) JD130Htz (MGI:5496674) (Aldhl1:L10a-eGFP)

value: dorsal hippocampus


title: 2017_547b: C1-PAP-GFP technical replicate 2

description: PAP, GFP, Animal C1, technical replicate 2

value: GFP


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G4_ad006


title: MTF2_SU-DIPG-XIII_(20180425_JS_HsDmSc_0330_JS257)

description: CUT&RUN for MTF2 in 1M SU-DIPG-XIII cells

source_name: SU-DIPG-XIII cells; anti-MTF2 Invitrogen PA535932

value: anti-MTF2 Invitrogen PA535932


title: R40RC: Patient #40 rectum stem cells-Control

value: rectum


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G3_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G4_ad004


title: IgG_VUMC_(20180608_JS_HsDmSc_0525_JS398)

description: CUT&RUN for IgG in 1M VUMC cells

source_name: VUMC cells; Rabbit IgG control abcam ab172730

value: VUMC cells

value: Rabbit IgG control abcam ab172730


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G3_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G4_ad010


title: SUZ12_SU-DIPG-IV_(20180425_JS_HsDmSc_0330_JS248)

description: CUT&RUN for SUZ12 in 1M SU-DIPG-IV cells

source_name: SU-DIPG-IV cells; anti-SUZ12 abcam ab12073

value: SU-DIPG-IV cells


title: MTF2_SU-DIPG-IV_(20180425_JS_HsDmSc_0330_JS249)

description: CUT&RUN for MTF2 in 1M SU-DIPG-IV cells

source_name: SU-DIPG-IV cells; anti-MTF2 Invitrogen PA535932


title: 2017_545c: C1-Astro-GFP technical replicate 3

description: Full Astrocytes, GFP, Animal C1, technical replicate 3


title: 2017_545a: C1-Astro-GFP technical replicate 1

description: Full Astrocytes, GFP, Animal C1, technical replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G2_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G12_ad004


title: IgG_SU-DIPG-IV_(20180425_JS_HsDmSc_0330_JS251)

description: CUT&RUN for IgG in 1M SU-DIPG-IV cells, replicate 1

source_name: SU-DIPG-IV cells; Rabbit IgG control abcam ab172730


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G12_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G2_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G2_ad006


title: IgG_SU-DIPG-XIII_rep2_(20180511_JS_HsSc_277_0413)

description: CUT&RUN for IgG in 1M SU-DIPG-XIII cells, replicate 2

source_name: SU-DIPG-XIII cells; Rabbit IgG control abcam ab172730


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G12_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G12_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G2_ad004


title: PBZT5

city: Milano

first: Eleonora

last: Lusito

address: Via Olgettina 60

country: Italy

institute: Ospedale San Raffaele

description: total RNA from single cell

data_processing:
Single-cell RNA sequencing computational analysis: raw sequencing data were preprocessed using the 10x Genomics Cell Ranger pipeline (v2.1.1). First, raw data were converted (i.e.demultiplexed) from BCLs to Cell Ranger compatible FSTQs using the cellranger mkfastq option with default parameters. Sequencing reads in FASTQ files for each replicate were then aligned to the reference mm10 genome with the Cell Ranger count option generating the bam file and the filtered genes-barcodes matrix (.mtx) containing only detected cellular barcodes. Downstream analysis including QC and exploration of single-cell RNA-seq data were performed using the R package Seurat v3.0.
Genome_build: mm10

source_name: Peripheral blood

extract_protocol:
Blood was taken through cardiac puncture with 1ml syringe attached to a 26g needle filled with 50µL of 0.5M EDTA. Samples were lysed in 1XRBC lysis buffer (eBioscience) for 4min. For BM cells, mice femurs were flushed using a 23–gauge needle in PBS containing 2mM EDTA and 2% fetal bovine serum (FBS) and passed through a 70–µm nylon mesh sieve. Spleens were harvested and homogenized into single-cell suspensions using 70–µm nylon mesh sieves and syringe plungers. Lungs  were harvested and cut dry into small pieces before digested in liberase TM (Roche) and DNase1 (Sigma) for 45min at 37 ̊C. Lung were then homogenized into single-cell suspensions using 70–µm nylon mesh sieves and syringe plungers.
cDNA Droplet-based digital 3′ end scRNA-Seq was performed on a Chromium Single-Cell Controller (10 × Genomics, Pleasanton, CA) using the Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s instructions. Briefly, blood, bone marrow, spleen and lung CD45+CD11b+ leukocyte suspensions were FACS sorted in an Aria II sorter (BD). Cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12–14 cycles).

tag: genotype

value: WT

value: Peripheral blood


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G11_ad004

value: CP

tag: Sex

value: male


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G11_ad001

tag: age


title: IgG_SU-DIPG-XIII_rep1_(20180425_JS_HsDmSc_0330_JS259)

description: CUT&RUN for IgG in 1M SU-DIPG-XIII cells, replicate 1


title: Spleen1

description: total RNA from single cell

source_name: Spleen

value: Spleen


title: Spleen2

description: total RNA from single cell


title: IgG_CB660_(20180608_JS_HsDmSc_0517_JS390)

description: CUT&RUN for IgG in 1M CB660 cells

source_name: CB660 cells; Rabbit IgG control abcam ab172730

value: CB660 cells


title: Lung2

description: total RNA from single cell

source_name: Lung

value: Lung


title: PBZT13_2

description: total RNA from single cell


title: PBZT13_1

description: total RNA from single cell


title: IgG_H1_(20180608_JS_HsDmSc_0531_JS403)

description: CUT&RUN for IgG in 1M H1 cells

source_name: H1 cells; Rabbit IgG control abcam ab172730

value: H1 cells


title: H3K27M_VUMC_(20180608_JS_HsDmSc_0525_JS393)

description: CUT&RUN for H3K27M in 1M VUMC cells

source_name: VUMC cells; anti-H3K27M abcam ab190631

value: anti-H3K27M abcam ab190631


title: 2017_545b: C1-Astro-GFP technical replicate 2

description: Full Astrocytes, GFP, Animal C1, technical replicate 2

source_name: dorsal hippocampus

value: Tg(Aldh1l1-eGFP/Rpl10a) JD130Htz (MGI:5496674) (Aldhl1:L10a-eGFP)

value: Full Astrocytes

value: Animal C1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G3_ad002

tag: brain region


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G11_ad006

tag: strain


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G10_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G4_ad002


title: IgG_U5_(20180608_JS_HsDmSc_0517_JS381)

description: CUT&RUN for IgG in 1M U5 cells

source_name: U5 cells; Rabbit IgG control abcam ab172730

value: U5 cells


title: Lung1

description: total RNA from single cell


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G10_ad002


title: H3K27M_SU-DIPG-XIII_rep2_(20180605_JS_HsSc_270_0413)

description: CUT&RUN for H3K27M in 1M SU-DIPG-XIII cells, replicate 2

source_name: SU-DIPG-XIII cells; anti-H3K27M abcam ab190631

value: SU-DIPG-XIII cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G10_ad001


title: BM2

description: total RNA from single cell

source_name: Bone Marrow

value: Bone Marrow


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G11_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G1_ad002


title: H3K27M_SU-DIPG-XIII_rep1_(20180425_JS_HsDmSc_0330_JS253)

description: CUT&RUN for H3K27M in 1M SU-DIPG-XIII cells, replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G1_ad006


title: BM1

description: total RNA from single cell


title: H3K27M_SU-DIPG-IV_rep2_(20180605_JS_HsSc_261_0413)

description: CUT&RUN for H3K27M in 1M SU-DIPG-IV cells, replicate 2

source_name: SU-DIPG-IV cells; anti-H3K27M abcam ab190631


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G1_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA180910_5J_1_CEMBA180910_5J_2_G1_ad004


title: H3K27M_SU-DIPG-IV_rep1_(20180425_JS_HsDmSc_0330_JS245)

description: CUT&RUN for H3K27M in 1M SU-DIPG-IV cells, replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F8_ad007


title: WT

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Sample demultiplexing and analyses were performed using Scanpy toolkit
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger v2.0 possorted_genome.bam BAM files and corresponding filtered gene barcodes matrices.

source_name: iNKT thymocytes

extract_protocol:
10x Genomics single-cell 3' V2 chemistry was used to generate single-cell emulsion.
Single-cell RNA-seq was performed following manufacturer’s protocol (Chromium™ Single Cell 3' Reagent Kit, V2 Chemistry) to obtain single cell 3’ libraries for Illumina sequencing.

treatment_protocol: Total invariant Natural Killer T cells were purified from mouse thymi (pool of 4 mice) of Fhl2+/+ or Fhl2-/- mice (5 week-old). Harvested thymi were mashed onto a 70 µm cell-strainer. Collection tube was centrifuged (400 xg, 4° for 6 min) and cells in the pellet were collected for cell sorting. Cells were resuspended at 20 x 10^6 cells per ml in FACS buffer containing 5 % of Fc block (2.4G2 supernatant) for 10 min on ice. After centrifugation, cells were suspended in antibody cocktail (Live Dead, anti-CD45, -CD3 and PBS57-CD1d tetramers) and incubated on ice for 25 min in the dark. After centrifugation, cells were resuspended in FACS buffer and subjected to cell sorting (FACS Aria, BD). iNKT thymocytes (Live Dead-, CD45+,  CD3+, Tetramer CD1d+) were sorted with a yield of purity > 98%.

value: invariant Natural Killer T cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F8_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F9_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F9_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F9_ad004


title: KO

value: KO


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F9_ad002


title: H3K27me3_U5_rep2_(20180608_JS_HsDmSc_0517_JS374)

description: CUT&RUN for H3K27me3 in 1M U5 cells, replicate 2

source_name: U5 cells; anti-H3K27me3 Cell Signaling 9733S

value: anti-H3K27me3 Cell Signaling 9733S


title: H3K27me3_VUMC_rep2_(20180410_JS_HsDmSc_0308_JS243)

description: CUT&RUN for H3K27me3 in 1M VUMC cells, replicate 2

source_name: VUMC cells; anti-H3K27me3 Cell Signaling 9733S

value: VUMC cells


title: Breast cancer cells, WT, 631 +Wnt3a_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

description: WT +Wnt3a_2

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using Bowtie2 and duplicate reads were removed by picard software
Peaks were identified from replicates using “getDifferentialPeaksReplicates.pl” option and further annotated using “annotatePeaks.pl” option are part of HOMER’s (Version 4.5) pipeline
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: Breast cancer cells, 631 +Wnt3a

growth_protocol: Pygo2 WT (+/+) and mutant (AE/AE) cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
75x10^3 cells were subjected to lysis and transposition reaction according to the protocol described previously (Buenrostro et al., 2015).
Barcoded libraries were prepared according to the protocol described previously (Buenrostro et al., 2015). 75x10^3 cells were used in each transposition reaction using the Nextera Tn5 Transposase kit (Illumina, FC-121-1030) followed by purification using Qiagen MinElute PCR purification kit (Qiagen, 28004). Transposed DNA fragments were PCR amplified over 13 cycles using barcoded PCR primers and NEB High Fidelity PCR Master Mix (NEB, M0541). Libraries were purified using QIAquick PCR purification kit (Qiagen, 28104) and sequenced with Illumina Illumina NextSeq 500.

treatment_protocol: For Wnt3a treatment, Pygo2 WT (+/+) and mutant (AE/AE) cell lines were treated with 100 ng/ml Wnt3a for 3 days. Medium was changed and fresh Wnt3a was added daily. Untreated cells served as control. For TGFb treatment, Pygo2 WT (+/+) and mutant (AE/AE) cell lines were treated with 2 ng/ml TGFb for 4 days. Medium was changed every second day with fresh addition of TGFb. Untreated cells served as control.

value: MMTV-PyMT (FVB/N)

value: Tumor developed in mammary gland 2/3

value: Breast cancer cells

tag: transgene

value: PyMT

value: Pygo2 +/+ (WT)

value: Wnt3a treated

tag: time

value: 3 days


title: Breast cancer cells, AE/AE, 828 -Wnt3a_2

description: AE/AE -Wnt3a_2

source_name: Breast cancer cells, 828 -Wnt3a

value: Pygo2 A342E/A342E knockin

value: UT


title: Breast cancer cells, AE/AE, 828 +Wnt3a_2

description: AE/AE +Wnt3a_2

source_name: Breast cancer cells, 828 +Wnt3a


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F8_ad001

data_processing:
Library strategy: snmC-seq2
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
Genome_build: 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

value: CP

value: male


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F7_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F7_ad004


title: H3K27me3_U5_rep1_(20180608_JS_HsDmSc_0517_JS373)

description: CUT&RUN for H3K27me3 in 1M U5 cells, replicate 1

value: U5 cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F7_ad001


title: Breast cancer cells, AE/AE, 828 +TGFb_2

description: AE/AE +TGFb_2

source_name: Breast cancer cells, 828 +TGFb

value: TGFb treated

value: 4 days


title: H3K27me3_VUMC_rep1_(20180410_JS_HsDmSc_0308_JS242)

description: CUT&RUN for H3K27me3 in 1M VUMC cells, replicate 1


title: Breast cancer cells, WT, 631 -Wnt3a_2

description: WT -Wnt3a_2

source_name: Breast cancer cells, 631 -Wnt3a


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F7_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F6_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F6_ad002


title: H3K27me3_SU-DIPG-XIII_rep2_(20180410_JS_HsDmSc_0308_JS239)

description: CUT&RUN for H3K27me3 in 1M SU-DIPG-XIII cells, replicate 2

source_name: SU-DIPG-XIII cells; anti-H3K27me3 Cell Signaling 9733S

value: SU-DIPG-XIII cells


title: H3K27me3_SU-DIPG-XIII_rep1_(20180410_JS_HsDmSc_0308_JS238)

description: CUT&RUN for H3K27me3 in 1M SU-DIPG-XIII cells, replicate 1

value: anti-H3K27me3 Cell Signaling 9733S


title: H3K27me3_SU-DIPG-IV_rep1_(20180410_JS_HsDmSc_0308_JS230)

description: CUT&RUN for H3K27me3 in 1M SU-DIPG-IV cells, replicate 1

source_name: SU-DIPG-IV cells; anti-H3K27me3 Cell Signaling 9733S

value: SU-DIPG-IV cells


title: H3K27me3_SU-DIPG-IV_rep2_(20180410_JS_HsDmSc_0308_JS231)

description: CUT&RUN for H3K27me3 in 1M SU-DIPG-IV cells, replicate 2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F6_ad001


title: H3K27me3_H1_rep2_(20180608_JS_HsDmSc_0531_JS400)

description: CUT&RUN for H3K27me3 in 1M H1 cells, replicate 2

source_name: H1 cells; anti-H3K27me3 Cell Signaling 9733S

value: H1 cells


title: Breast cancer cells, AE/AE, 828 -TGFb_2

description: AE/AE -TGFb_2

source_name: Breast cancer cells, 828 -TGFb

value: MMTV-PyMT (FVB/N)

value: Tumor developed in mammary gland 2/3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F6_ad006


title: Breast cancer cells, AE/AE, 828 +Wnt3a_1

description: AE/AE +Wnt3a_1

value: Breast cancer cells

value: PyMT


title: Breast cancer cells, WT, 631 +TGFb_2

description: WT +TGFb_2

source_name: Breast cancer cells, 631 +TGFb

value: Pygo2 +/+ (WT)


title: H3K27me3_H1_rep1_(20180608_JS_HsDmSc_0531_JS399)

description: CUT&RUN for H3K27me3 in 1M H1 cells, replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F5_ad004


title: Breast cancer cells, AE/AE, 828 -Wnt3a_1

description: AE/AE -Wnt3a_1

value: 3 days


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F5_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F5_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F4_ad008


title: Breast cancer cells, WT, 631 -TGFb_2

description: WT -TGFb_2

source_name: Breast cancer cells, 631 -TGFb


title: H3K27me3_CB660_rep2_(20180608_JS_HsDmSc_0517_JS383)

description: CUT&RUN for H3K27me3 in 1M CB660 cells, replicate 2

source_name: CB660 cells; anti-H3K27me3 Cell Signaling 9733S

value: CB660 cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F4_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F4_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F3_ad006


title: H3K27me3_CB660_rep1_(20180608_JS_HsDmSc_0517_JS382)

description: CUT&RUN for H3K27me3 in 1M CB660 cells, replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F3_ad001


title: Breast cancer cells, WT, 631 +Wnt3a_1

description: WT +Wnt3a_1

value: Wnt3a treated


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F4_ad002

value: CP


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F3_ad002

value: male


title: H3K27ac_U5_rep2_(20180608_JS_HsDmSc_0517_JS379)

description: CUT&RUN for H3K27ac in 1M U5 cells, replicate 2

source_name: U5 cells; anti-H3K27ac Millipore MABE647

value: U5 cells

value: anti-H3K27ac Millipore MABE647


title: Breast cancer cells, WT, 631 -Wnt3a_1

description: WT -Wnt3a_1

value: UT


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F2_ad004

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F2_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F2_ad002


title: Breast cancer cells, AE/AE, 828 -TGFb_1

description: AE/AE -TGFb_1

value: Pygo2 A342E/A342E knockin

value: 4 days


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F12_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F2_ad001


title: Breast cancer cells, WT, 631 +TGFb_1

description: WT +TGFb_1

value: TGFb treated


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F12_ad004


title: H3K27ac_SU-DIPG-XIII_(20180511_JS_HsSc_276_0413)

description: CUT&RUN for H3K27ac in 1M SU-DIPG-XIII cells

source_name: SU-DIPG-XIII cells; anti-H3K27ac Millipore MABE647

value: SU-DIPG-XIII cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F12_ad002


title: Breast cancer cells, WT, 631 -TGFb_1

description: WT -TGFb_1

value: MMTV-PyMT (FVB/N)


title: AE/AE: 828 +Wnt3a_2

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to MM10 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in quasR and CPM (counts per million) was computed for each sample
Genome_build: mm10
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: Tumor developed in mammary gland 2/3

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions.
200 ng of RNA was processed with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). Library QC was performed with a Fragment Analyzer (AATI) using the Standard Sensitivity NGS Fragment Analysis Kit (DNF-473). RNA-Seq libraries were sequenced with the SR75 with NextSeq (Illumina).

tag: mutation

value: Wnt3a treated (3 days)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F12_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F12_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F3_ad007


title: H3K27ac_H1_rep2_(20180608_JS_HsDmSc_0531_JS402)

description: CUT&RUN for H3K27ac in 1M H1 cells, replicate 2

source_name: H1 cells; anti-H3K27ac Millipore MABE647

value: H1 cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F3_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F11_ad004


title: H3K27ac_CB660_rep2_(20180608_JS_HsDmSc_0517_JS388)

description: CUT&RUN for H3K27ac in 1M CB660 cells, replicate 2

source_name: CB660 cells; anti-H3K27ac Millipore MABE647


title: H3K27ac_H1_rep1_(20180608_JS_HsDmSc_0531_JS401)

description: CUT&RUN for H3K27ac in 1M H1 cells, replicate 1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F11_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F11_ad001


title: AE/AE: 828 -Wnt3a_2

value: Breast cancer cells

value: PyMT

value: UT (3 days)


title: H3.3_SU-DIPG-IV_(20180220_JS_HsSc_020618_JS228)

description: CUT&RUN for H3.3 in 1M SU-DIPG-IV cells

source_name: SU-DIPG-IV cells; anti-H3.3 Abnova H00003021-M01

value: SU-DIPG-IV cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F11_ad012


title: H3K27ac_SU-DIPG-IV_(20180605_JS_HsSc_267_0413)

description: CUT&RUN for H3K27ac in 1M SU-DIPG-IV cells

source_name: SU-DIPG-IV cells; anti-H3K27ac Millipore MABE647


title: Breast cancer cells, AE/AE, 828 +TGFb_1

description: AE/AE +TGFb_1

source_name: Breast cancer cells, 828 +TGFb

value: Tumor developed in mammary gland 2/3


title: H3K27ac_U5_rep1_(20180608_JS_HsDmSc_0517_JS378)

description: CUT&RUN for H3K27ac in 1M U5 cells, replicate 1


title: WT: 631 +Wnt3a_2

value: Pygo2 +/+ (WT)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F10_ad002

value: CP

value: male


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F10_ad004


title: AE/AE: 828 -TGFb_2

value: UT (4 days)


title: AE/AE: 828 +TGFb_2

value: TGFb treated (4 days)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F10_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F10_ad007


title: WT: 631 +TGFb_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F1_ad001


title: H3K27ac_CB660_rep1_(20180608_JS_HsDmSc_0517_JS387)

description: CUT&RUN for H3K27ac in 1M CB660 cells, replicate 1

value: CB660 cells

value: anti-H3K27ac Millipore MABE647


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F1_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F1_ad012


title: WT_p852_AHT3

city: Wuerzburg

first: Martin

last: Fraunholz

address: Theodor-Boveri-Weg

department: Chair of Microbiology

institute: University of Wuerzburg

data_processing:
Adapters were removed using cutadapt.
Reads were mapped using Bowtie2, and were indexed with Samtools.
bedtools and featureCount was used to generate gene coverages
DEseq2 was used to identify differentially expressed genes.
Genome_build: NC_022222.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each alignment.

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: Bacteria were grown in 10 ml Tryptic soy broth (TSB) in 100 ml Erlenmeyer flask at 37 C (250 rpm orbital shaker).

extract_protocol:
Bacteria were harvested by centrifugation and RNA was isolated by bead beating (FastPrep, Lysis matrix B) with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 200 ng/ml anhydrous tetracycline were added to wild-type bacteria without (control) and with the plasmid contining the ORF RSAU_000852 under control of the Ptet/xyl promoter.

value: transgene

tag: induction

value: induced


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F1_ad006

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: CEMBA180910_5J_1_CEMBA180910_5J_2_E9_ad008


title: WT_p852_AHT2


title: WT_p852_AHT1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E9_ad007


title: mut_3

value: mutant

value: uninduced


title: WT: 631 -Wnt3a_2

value: MMTV-PyMT (FVB/N)


title: WT: 631 -TGFb_2

value: Breast cancer cells


title: CEMBA180910_5J_1_CEMBA180910_5J_2_F10_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E9_ad001


title: AE/AE: 828 +Wnt3a_1

value: PyMT

value: Pygo2 A342E/A342E knockin

value: Wnt3a treated (3 days)


title: mut_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E9_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E9_ad006


title: AE/AE: 828 -Wnt3a_1

value: UT (3 days)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E8_ad006


title: mut_1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E8_ad001


title: WT: 631 +Wnt3a_1

value: Pygo2 +/+ (WT)


title: WT_AHT_3

value: wild-type


title: WT: 631 -Wnt3a_1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E7_ad002

value: CP

value: male


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E7_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E6_ad006


title: WT_AHT_1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E7_ad001


title: AE/AE: 828 +TGFb_1

value: TGFb treated (4 days)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E6_ad002


title: WT_AHT_2


title: AE/AE: 828 -TGFb_1

value: UT (4 days)


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E5_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E5_ad001


title: WT_3


title: WT: 631 -TGFb_1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E5_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E5_ad006


title: WT_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E4_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E4_ad001


title: U1_input_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peakcalling with  default parameters
Genome_build: GRCm38

source_name: mouse neuroblastoma N2a cells

growth_protocol: N2a cells were grown in DMEM supplemented with 10% (vol/vol) FBS (Gibco) and antibiotics (penicillin and streptomycin) (Beyotime) at 37°C.

extract_protocol:
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of RIPA buffer( 50 mM Tris 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate).The cells lysates was sonicated to generate DNA fragments of 200-500 bp, centrifuged for 10 min at 12,000 g, and the supernatant was directly used for immunoprecipitation. Place the tube containing the Pierce™ ChIP-grade Protein A/G Magnetic Beads on the magnetic ,then, discard the supernatant. Wash the beads for three times with 1ml 0.1M sodium phosphate Buffer .
ChIP-seq was performed by using ThruPLEX® DNA-seq kit (R400427; Rubicon Genomics) according to manufacturer’s instructions. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 oC until used for sequencing. ChIP-Seq sequencing was performed on NextSeq500 platform with 151 bp paired-end sequencing.

treatment_protocol: After seeding, cells were incubated for 12 h at 37°C. Plasmids expressing lncRNA was transfected into cells by using Lipo3000 (Invitrogen).

value: neuroblastoma

tag: chip antibody


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E4_ad004


title: U1_input_2


title: YTK47-6-Glc120_rep

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

institute: Korea Institute of Science and Technology Information

data_processing:
Quality control using FastQC v0.10.1
Alignment using TopHat v2.0.13 to S. cerevisiae reference genome (EF4) with option of -fr-firststrand
Expression quantification using Cufflinks v2.2.1
Genome_build: EF4 (Ensembl relsease 74)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

organism: Saccharomyces cerevisiae

source_name: Yeast cell

growth_protocol: Cells were pre-cultured in SC-media containing raffinose until mid-log phase and then shifted to SC-media containing galactose (120 min) for the 1st galactose exposure. After 120 min, the cells were transferred to SC-glucose for 120 min and back to SC-galactose (15 and 30 min) for the 2nd galactose exposure.

extract_protocol:
Total RNA was isolated from cells with hot phenol.
Libraries was constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) after ribosomal RNA was depleted using the Ribo-Zero yeast kit (Epicenter).

value: Yeast cell

tag: Stage

value: yng1 deletion


title: YTK47-5-Glc30_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E4_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E3_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E3_ad002


title: U1_H3K27_1

value: H3K27me3 (Millipore,07-449)


title: YTK47-4-Gal120_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E3_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E3_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E2_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E5_ad007


title: WT: 631 +TGFb_1


title: YTK47-2-Gal15_rep


title: NC_input_1


title: YTK47-1-Ra0_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E2_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E2_ad002


title: WT_1

value: uninduced


title: NC_H3K27_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E4_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E12_ad001


title: YSB787-6-Glc120_rep

value: wildtype


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E12_ad004


title: NC_H3K27_1


title: U1_H3K27_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E12_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E2_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E3_ad004


title: YSB787-5-Glc30_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E12_ad002


title: YTK47-3-Gal30_rep


title: NC_input_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E11_ad006


title: YSB787-3-Gal30_rep


title: C2_0h

description: RNA-Seq_CellLine_basic_lncrna_all_expressed_gene_RPKM.txt

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with pvalue < =0.01 and fold change >=2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

source_name: N2a cell line

extract_protocol:
Total RNA was extracted by using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, and RQ1 DNase (Promega, Madison, WI, USA) was used to remove contaminating genomic DNA. The quality and quantity of the purified RNA was monitored at the ratios of A260/A280 and A260/230 on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 5ug of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 300-500 bps were purified, quantified and stored at -80 oC until used for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina Next500 system for 150 nt pair-end sequencing by ABlife. Inc (Wuhan, China)。

value: mouse neuroblastoma

value: Wild Type


title: C3_0h


title: C1_0h


title: YSB787-2-Gal15_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E11_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E10_ad002


title: B2C3d3_72h

value: RABV infection


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E10_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E10_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E10_ad012


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E1_ad006


title: YSB787-1-Ra0_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E10_ad001


title: YTK47-8-Gal30


title: B2C3d1_72h


title: B2C3d2_72h


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D9_ad004


title: B2C2d3_48h


title: YTK47-7-Gal15


title: YSB787-4-Gal120_rep


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E1_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E11_ad002


title: B2C2d2_48h


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E1_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D9_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D9_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_E11_ad004


title: YTK47-6-Glc120


title: YTK47-4-Gal120


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D8_ad004


title: YTK47-5-Glc30


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D8_ad002


title: B2C2d1_48h


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D8_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D9_ad001


title: YTK47-3-Gal30


title: B2C1d3_24h


title: B2C1d2_24h


title: YTK47-2-Gal15


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D7_ad004


title: B2C1d1_24h


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D7_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D7_ad006


title: AH3d3_72h


title: YTK47-1-Ra0


title: YSB787-7-Gal15


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D6_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D6_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D6_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D7_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D6_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D6_ad007


title: AH3d1_72h


title: YSB787-8-Gal30


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D5_ad002


title: YSB787-6-Glc120


title: AH2d2_48h


title: AH2d4_48h


title: YSB787-5-Glc30


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D8_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D5_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D4_ad006


title: AH2d1_48h


title: YSB787-4-Gal120


title: YSB787-3-Gal30


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D4_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D4_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D4_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D5_ad004


title: AH1d3_24h


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D3_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D3_ad001


title: AH3d2_72h


title: YSB787-2-Gal15


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D3_ad002


title: YSB787-1-Ra0


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D3_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D3_ad006


title: AH1d1_24h


title: AH1d2_24h


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D2_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D2_ad001


title: Y_sCMB_99: Young_Subject-sCMB99

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

data_processing:
Total RNA was sequenced on an Illumina HiSeq 4000 system, using a standard paired-end 150 bp dual indexing protocol. The two sets of samples (University of Kentucky and University of Alabama), each containing samples from all timepoints of both placebo and metformin arm as well as young, were sequenced in different batches that were corrected for in the downstream analyses (see batch).
Raw fastq sequence reads were passed through quality control using FastQC (0.11.4) and the QC results were compiled for all samples using MultiQC (1.7).
Raw fastq files were trimmed for adapter sequences, filtered for low quality reads and short reads, using the default parameters in fastp (0.19.4)
After checking for QC, RNA-Sequencing by Expectation Maximization- RSEM (1.3.0) in conjunction with the STAR aligner (2.6.1b) was used to align the raw reads to the hg38 primary assembly build of the reference human genome, with transcript annotations (gencode.v29.annotation.gtf) downloaded from GENCODE
All statistical analysis for the gene expression data were carried out using the R statistical software (R-3.6.0)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample (generated using RSEM)

source_name: Vastus lateralis muscle

extract_protocol:
Approximately 35 mg of muscle was subjected to bead homogenization in Qiazol and RNA purified using miRNeasy Mini Kits and stored at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vastus lateralis muscle

tag: study arm

value: Young

tag: biopsy

tag: batch


title: Y_sCMB_91: Young_Subject-sCMB91

tag: tissue


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D2_ad002

city: La Jolla

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D12_ad002


title: C2_0d

description: RNA-Seq_tissue_basic_expressed_gene_RPKM.txt

source_name: brain tissue

tag: type

value: Tissue

value: AH


title: Y_sCMB_87: Young_Subject-sCMB87


title: Y_sCMB_83: Young_Subject-sCMB83


title: B6_52_6d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D2_ad006

value: CP


title: C1_0d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D12_ad006

value: male


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D12_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D11_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D11_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D10_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D12_ad004


title: Y_sCMB_90: Young_Subject-sCMB90


title: C3_0d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D10_ad002


title: Y_sCMB_82: Young_Subject-sCMB82


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D11_ad004


title: Y_sCMB_65: Young_Subject-sCMB65


title: Y_sCMB_79: Young_Subject-sCMB79


title: B6_51_6d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C9_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D10_ad004


title: B43_4d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D1_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C9_ad012


title: Y_sCMB_71: Young_Subject-sCMB71


title: Y_sCMB_56: Young_Subject-sCMB56


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C9_ad008


title: B42_4d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D1_ad004


title: B6_53_6d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C8_ad007


title: Y_sCMB_73: Young_Subject-sCMB73


title: B1_2d


title: B3_2d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_D10_ad001


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C6_ad008


title: B41_4d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C7_ad010


title: Y_sCMB_1: Young_Subject-sCMB1


title: A6_53_6d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C5_ad002


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C6_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C5_ad004


title: Y_sCMB_20: Young_Subject-sCMB20


title: B2_2d


title: A6_52_6d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C4_ad004


title: A6_51_6d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C5_ad006


title: Y_sCMB_112: Young_Subject-sCMB112


title: Y_sCMB_123: Young_Subject-sCMB123


title: Y_sCMB_18: Young_Subject-sCMB18


title: A43_4d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C5_ad008


title: A5_2d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C3_ad006


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C4_ad006


title: Y_sCMB_116: Young_Subject-sCMB116


title: A42_4d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C7_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C7_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C4_ad002


title: A3_2d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C3_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C3_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C4_ad007


title: Y_sCMB_24: Young_Subject-sCMB24


title: A41_4d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C2_ad008


title: pcDNA3_1_U1_48h_2

description: result_origin_basic_expressed_gene_RPKM.txt

tag: cell line

value: RABV infection and RVRL1 overexpression


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C2_ad007


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C4_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C12_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C3_ad004


title: M_41_1: metPRT_Subject-41_Biopsy-1

value: metPRT


title: pcDNA3_1_U1_48h_1

tag: genotype


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C12_ad007

tag: Sex


title: Y_sCMB_106: Young_Subject-sCMB106


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C11_ad004

tag: age


title: Y_sCMB_101: Young_Subject-sCMB101


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C6_ad007

tag: brain region


title: pcDNA3_1_U1_24h_1

tag: strain


title: A4_2d


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C11_ad012


title: pcDNA3_1_48h_2


title: Y_sCMB_107: Young_Subject-sCMB107


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C2_ad004


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C11_ad008


title: pcDNA3_1_48h_1


title: M_7_3: metPRT_Subject-7_Biopsy-3


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C10_ad006


title: M_7_1: metPRT_Subject-7_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C12_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C10_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C12_ad012


title: pcDNA3_1_U1_24h_2


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C1_ad008


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C11_ad010


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C1_ad006


title: M_35_1: metPRT_Subject-35_Biopsy-1


title: CEMBA180910_5J_1_CEMBA180910_5J_2_C11_ad007


title: M_33_3: metPRT_Subject-33_Biopsy-3