title: SARS-CoV-2 titration - water - rep2

status: Public on Apr 15 2021

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GGTTATCG-GTCTGTCT.gz
210414.RWT.Bonasio.sample24

data_processing:
library strategy: COV-ID
Reads were filtered for optical quality using FASTX-toolkit utility fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/), then cutadapt45 was used to remove adapters and demultiplex LAMP barcodes.
Genome_build: Reads were aligned to a custom index containing SARS-CoV-2 genome (NC_045512.2), Influenza H1N1 coding sequences (NC_026431.1, NC_026432.1, NC_026433.1, NC_026434.1, NC_026435.1, NC_026436.1, NC_026437.1, NC_026438.1), STATH coding sequence (NM_003154.3), and custom N2 spike sequence.
Supplementary_files_format_and_content: Tab-delimited text files containing summaries of aligned raw reads to control sequences and viral genomes for each experiment

organism: blank sample

source_name: Water

growth_protocol: Saliva was harvested from human donors

extract_protocol:
We prepared 100x TCEP/EDTA buffer (250 mM TCEP, 100 mM EDTA, 1.15 N NaOH) 29. TCEP/EDTA buffer was added to human saliva at 1:100 volume, then samples were capped, vortexed to mix and heated in a thermocycler (95ºC 5 min, 4ºC hold) until ready to use for RT-LAMP.
1 μL of diluted LAMP material was used as a template for PCR using OneTaq DNA polymerase (NEB Cat. M0480L) with 100 nM each of custom dual-indexed Illumina P5 and P7 primers in either 10 or 25 μL reaction. PCR reactions were incubated as follows: (25 cycles of stage 1 [94ºC x 15 sec, 45ºC x 15 sec, 68ºC x 10 sec], 10 cycles of Stage 2 [ 94ºC x 15 sec, 68ºC x 10 sec], 68ºC x 1 min, 4ºC  x ∞).

treatment_protocol: Heat-inactivated SARS-CoV-2 (BEI Resources Cat. NR-52286) or H1N1 genomic RNA (Twist Biosciences Cat. 103001) was added to inactivated saliva prior to RT-LAMP.

value: COV-ID

tag: virus added

tag: experiment

value: titration

tag: viral concentration


title: SARS-CoV-2 titration - 5 - rep1

type: SRA

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.TCATGACG-GATTCCAG.gz
210414.RWT.Bonasio.sample19

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Saliva

tag: technology


title: SARS-CoV-2 titration - 5 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.ACACGTGT-AGCAATGG.gz
210414.RWT.Bonasio.sample20


title: RNAseq - untagged ESCs day 0 - untreated - rep1

status: Public on Apr 21 2021

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0101
B6T1.NT.ESC.b1

data_processing:
Paired-end RNA-seq reads were aligned the Mus musculus mm10 genome using STAR 2.6.1d (Dobin et al., 2013) with default parameters except –peOverlapNbasesMin set to 10 and –alignIntronMax set to 100000.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-separated file containg TPMs (transcripts per million) for each NCBI annotated gene with a gene symbol.

molecule: polyA RNA

organism: Mus musculus

source_name: ESCs

growth_protocol: C57BL/6 mouse ESCs (ATCC) were cultured on gelatinized dishes in serum-free N2B27 media  (1:1 mix of neurobasal medium (Gibco) and DMEM/F12 (Gibco), 100 mM MEM nonessential amino acids (Sigma), 55 µM 2-mercaptoethanol (Gibco), 2 mM L-glutamine (Sigma), 0.5% penicillin/streptomycin (Sigma), 1x N27 and 1x B27 (Gibco)) supplemented with 100 U/mL leukemia inhibitory factor (LIF) (Chemicon), 3 µM CHIR99021 (Millipore) and 1 µM PD0325901 (Millipore). Cells were passaged every 2–3 days via dissociation in 0.05% trypsin (Genesee Scientific). Differentiation to NPCs was performed as follows. ESCs were seeded in serum-free conditions at a density of 15,000 cells/mL and incubated for 12 h to allow for cell attachment. For NPC induction, the ESC media was removed and replaced with N2B27 media supplemented with 40 µg/mL BSA (Sigma) and 10 ng/mL bFGF (R&D Biosystems), and incubated for 72 h with daily media exchanges, then media was replaced with N2B27 media supplemented with 40 µg/mL BSA (Sigma) and 500 nM SAG (Millipore) for an additional 48 h before harvesting for RNA, chromatin, or western blot analysis.

extract_protocol:
Cells were rinsed once with PBS and lysed via direct addition of TRIzol reagent (Thermo Fisher Scientific). Total cellular RNA was purified using the Direct-zol RNA Miniprep kit (Zymo Research).
PolyA+ RNA was isolated from 500 ng total RNA using Dynabeads Oligo(dT)25 beads (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method. UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter) and quantified by qPCR before and after amplification.

treatment_protocol: To induce degradation of AID-tagged proteins (SUZ12, MTF2. or JARID2), indole-3-acetic acid (IAA, chemical analog of auxin) was added to the cell culture medium at a final concentration of 50 µM from a 500 mM stock dissolved in sterile water that was stored long-term at -20ºC.

tag: strain

tag: genotype

value: untagged, Tir1

tag: treatment

value: untreated

tag: length of treatment

value: 12 hours


title: RNAseq - untagged ESCs day 0 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b1010
B6T1.IAA.ESC.b1

value: auxin


title: SARS-CoV-2 + FLU matrix - pool 1

description:
processed data file:
SARS.flu.count.table.tsv
201125.H3NFMBGXH.b1005.R1.gz
210414.RWT.Bonasio.sample26

value: SARA-CoV-2 + H1N1

value: SARS + flu

value: variable


title: RNAseq - untagged ESCs day 0 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0202
B6T1.NT.ESC.b2


title: Paper-based COV-ID - pool 2

description:
processed data file:
paper.based.count.table.tsv
210408.AH2Y2NBGXJ.RB706.R1.gz
210414.RWT.Bonasio.sample30

value: paper-based


title: Clinical samples - COV-ID pool

description:
processed data file:
FGC2164_s_1_1_TACGCTAG-GACATGAT.fastq.gz
210414.RWT.Bonasio.sample25

value: clinical

value: unknown


title: Paper-based COV-ID - pool 1

description:
processed data file:
paper.based.count.table.tsv
210408.AH2Y2NBGXJ.RB712.R1.gz
210414.RWT.Bonasio.sample29


title: SARS-CoV-2 titration - water - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.TACGCTAG-CTTCCTTC.gz
210414.RWT.Bonasio.sample23


title: SARS-CoV-2 titration - 0 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GAGGTAAC-ACGTTAGC.gz
210414.RWT.Bonasio.sample21


title: SARS-CoV-2 titration - 0 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.AGGCCATT-ATTCGGCA.gz
210414.RWT.Bonasio.sample22


title: SARS-CoV-2 + FLU matrix - pool 2

description:
processed data file:
SARS.flu.count.table.tsv
210316.AHVTTVBGXH.b1002.R1.gz
210414.RWT.Bonasio.sample27


title: SARS-CoV-2 titration - 10 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GAATTGTG-ACGAAGCC.gz
210414.RWT.Bonasio.sample18


title: SARS-CoV-2 + FLU matrix - pool 3

description:
processed data file:
SARS.flu.count.table.tsv
210316.AHVTTVBGXH.b1208.R1.gz
210414.RWT.Bonasio.sample28

value: variabe


title: RNAseq - SUZ12-AID ESCs day 0 - auxin - rep1

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0507
S12AID.IAA.ESC.b1

value: SUZ12-AID, Tir1


title: SARS-CoV-2 titration - 20 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.ACAGCACA-ATCGCATT.gz
210414.RWT.Bonasio.sample15


title: SARS-CoV-2 titration - 20 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GTACGATG-AGTGTGAG.gz
210414.RWT.Bonasio.sample16


title: SARS-CoV-2 titration - 10 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GTAGGTGC-TGCGTTCT.gz
210414.RWT.Bonasio.sample17


title: RNAseq - untagged ESCs day 0 - untreated - rep3

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0303
B6T1.NT.ESC.b3


title: SARS-CoV-2 titration - 40 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.AGCGTACT-GACATGAT.gz
210414.RWT.Bonasio.sample14


title: SARS-CoV-2 titration - 40 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.CTGTGTCA-GCATGATA.gz
210414.RWT.Bonasio.sample13


title: SARS-CoV-2 titration - 80 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.AGCGTACT-CTTCCTTC.gz
210414.RWT.Bonasio.sample11


title: SARS-CoV-2 titration - 80 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.CTGTGTCA-GTCTGTCT.gz
210414.RWT.Bonasio.sample12


title: SARS-CoV-2 titration - 160 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.ACAGCACA-ATTCGGCA.gz
210414.RWT.Bonasio.sample10


title: SARS-CoV-2 titration - 320 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GTAGGTGC-AGCAATGG.gz
210414.RWT.Bonasio.sample08


title: SARS-CoV-2 titration - 320 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GAATTGTG-GATTCCAG.gz
210414.RWT.Bonasio.sample07


title: SARS-CoV-2 titration - 160 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GTACGATG-ACGTTAGC.gz
210414.RWT.Bonasio.sample09


title: SARS-CoV-2 titration - 640 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.TCATGACG-ACGAAGCC.gz
210414.RWT.Bonasio.sample06


title: SARS-CoV-2 titration - 1280 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GAGGTAAC-AGTGTGAG.gz
210414.RWT.Bonasio.sample04


title: SARS-CoV-2 titration - 10000 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.GGTTATCG-GCATGATA.gz
210414.RWT.Bonasio.sample01


title: SARS-CoV-2 titration - 10000 - rep2

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.TACGCTAG-GACATGAT.gz
210414.RWT.Bonasio.sample02


title: Pre_22.029 (RS-02948647)

status: Public on Dec 28 2020

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Fastq files generated with CASAVA
fastq files mapped to hg38 with STAR aligner
gene count levels obtained from STAR
Voom normalized counts using limma
Genome_build: hg38
Supplementary_files_format_and_content: voom normalized counts in csv format

source_name: tumor sample

extract_protocol:
RNA was extracted with Qiagen columns
The sequencing libraries were prepared with TruSeq Stranded Total RNA kit (Illumina Inc), from 500ng total RNA. Following manufacturer’s instructions

tag: tissue

value: ovarian cancer

tag: condition

value: pre treatment

tag: specimen

tag: time point


title: HUDEP2_ATACseq_rep3

status: Public on Feb 04 2021

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: ATAC-seq

library_source: genomic

data_processing:
Two mutant clones and Hupde1 and Hudep2 samples were mapped to hg19 using BWA mem (v0.7.16a).
Duplicated reads were removed with samtools (v0.17). ATAC-seq peaks were called using MACS2 (v2.1.1) with the following parameters: macs2 callpeak --nomodel --shift --100 --extsize 200. BigWiggle files were generated using DeepTools (v3.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

molecule: genomic DNA

extract_protocol:
The ATAC-seq library was prepared according to the published omni-ATAC protocol, using 50,000 live cells per sample
Libraries were pair-end 100-bp sequenced using an Illumina HiSeq 4000 system.

tag: cell line


title: HUDEP2_ATACseq_rep1

description: ATAC-seq


title: HUDEP1_ATACseq_rep3

description: ATAC-seq


title: HUDEP1_ATACseq_rep1

description: ATAC-seq


title: Pre_22.022 (RS-02948645)


title: Pre_58.007 (RS-02948643)


title: Pre_22.026 (RS-02948646)


title: Pre_58.008 (RS-02948644)


title: Pre_58.003 (RS-02948641)


title: Pre_58.006 (RS-02948642)


title: Pre_58.001 (RS-02948640)


title: SARS-CoV-2 titration - 1280 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.AGGCCATT-ATCGCATT.gz
210414.RWT.Bonasio.sample03


title: Post_58.008 (RS-02948638)

value: post epacadostat


title: Post_58.003 (RS-02948639)


title: SARS-CoV-2 titration - 640 - rep1

description:
processed data file:
titration.count.table.tsv
200901.FGC2160.ACACGTGT-TGCGTTCT.gz
210414.RWT.Bonasio.sample05

value: COV-ID


title: VCaP_2

status: Public on Dec 31 2020

city: Göttingen

first: Oliver

last: Hahn

address: Robert-Koch-Str. 40

department: Department of Urology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Base calling was done using the BaseCaller to bcl files function in the Illumina software.
De-multiplexing was done using bcl2fastq (version 2.17.1.14).
Fastq files were then mapped to the human transcriptome (UCSC HG19) using TopHat2 (version 2.1.0) with very sensitive Bowtie2 settings
Differential gene expression was assessed with the Cuffdiff function of the Cufflinks package (version 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements resulting from cuffdiff analysis of VCaP samples vs. VCaPrev samples

growth_protocol: Cells were cultured in phenol-red free DMEM with 10% fetal bovine serum (both Sigma Aldrich, Taufkirchen, Germany). For the experiments, cells were kept under 35 passages and confluence was kept under 80%.

extract_protocol:
Total RNA was extracted using Trizol extraction and quantified with a Qubit 3 fluorometer. RNA quality was checked on a 1.5% agarose gel. 1 µg of total RNA was then used for library preparation.
Library preparation was done with a total amount of 1 µg RNA per sample using the TruSeq RNA Library Prep Kit v2 (Illumina Inc., San Diego, CA, USA). Size range was verified to be around 280 bp using BioAnalyzer 2100 (Agilent Technologies. Santa Clara, CA, USA). Sequencing was done at the NGS core facility (NIG) at the University Medical Center Göttingen on an Illumina HiSeq 4000 platform

treatment_protocol: Androgen-dependent VCaPrev cells were kept with 1 nM Testosterone over 20 passages. Control cells were grown in normal DMEM media.

tag: cell line background

value: VCaP

tag: cell type

value: prostate cancer cell line

value: control media


title: Post_58.007 (RS-02948637)


title: VCaP_1


title: HUDEP1_ATACseq_rep2

description: ATAC-seq


title: HUDEP2_ATACseq_rep2

description: ATAC-seq


title: Post_22.029 (RS-02948634)


title: Post_58.001 (RS-02948635)


title: Post_58.006 (RS-02948636)


title: Post_22.022 (RS-02948632)


title: RNA_WT_P14_Cl13_D20_StemLike_3

status: Public on Dec 14 2020

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description: RNAseq_WT_P14_Cl13_D20_StemLike_Terminally_exhausted_RPKM.txt

data_processing:
Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm10 using TopHat 2.1.0.
RPKM calculated using Partek 6.6
Genome_build: mm10
Supplementary_files_format_and_content: Text files, RPKM values

source_name: CD8 P14

extract_protocol:
Cells from spleen were obtained by mechanical disruption. Isolated cells were further sorted based on their surface markers.
50,000 P14 cells were sorted and resuspended in Qiazol (Qiagen). Total RNA was extracted with miRNeasy Mini kit (Qiagen). mRNA was selected using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). RNAseq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for (NEB) according to manufacturer’s instruction.
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on a HiSeq 3000  according to the manufacturer's protocols.

treatment_protocol: Mice were intravenously (i.v.) injected with 2×106 PFU LCMV clone 13.

value: Spleen

tag: sorting marker

tag: culture condition

value: ex vivo

tag: infection

value: 20 days after LCMV Cl13 infection


title: RNA_WT_P14_Cl13_D20_StemLike_2


title: RNA_WT_P14_Cl13_D20_Terminally_exhausted_3


title: RNA_WT_P14_Cl13_D20_StemLike_1


title: RNA_WT_P14_Cl13_D20_Terminally_exhausted_1


title: sRNA - Tet2 KO - exp2 rep3

status: Public on Nov 18 2020

description:
tRF.counts.tsv.gz
KO.sRNA.e2b3

data_processing:
CLIP: AdapterRemoval (adapter sequence removal); UMI-tools (de-duplicate using UMI); STAR v 2.5.3a (alignment); DEGseq (map to gene models).
RIP: AdapterRemoval (adapter sequence removal); STAR v 2.5.3a (alignment); DEGseq (map to gene models).
small RNA: cutadapt (adapter sequence removal); fastx toolkit (quality filter; collapse reads to generate read counts); note: 3' tRNA-derived fragments do not align against genomic tRNAs without clipping CCA-tail (use bowtie2-2.2.6 or higher for correct random alignment of multimapping reads)
Genome_build: mm10
Supplementary_files_format_and_content: We provide tab-separated (tsv) count tables for each separate experiment (CLIP, RIP, sRNA-seq)

source_name: mESCs

growth_protocol: Cells were cultured on gelatin-coated dishes in KnockOut DMEM supplemented with 15% FBS, 100 mM MEM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, 0.5% Penicillin Streptomycin, 100 U/mL leukemia inhibitory factor (LIF), 3 µM CHIR99021 and 1 µM PD0325901. (Millipore)

extract_protocol:
Trizol, TBE urea PAGE size selection 14-38 nt
NEBNext® Small RNA

treatment_protocol: For CLIP, cells were pulsed with 500 µM 4SU for 4 hours and crosslinked with 400 mJ/cm2 UVB. For RIP and small RNA sequencing cells were left untreated.

value: Tet2 KO

tag: experiment

value: small RNA-seq

tag: molecule subtype

tag: internal ref


title: sRNA - Tet2 KO - exp2 rep1

description:
tRF.counts.tsv.gz
KO.sRNA.e2b1

tag: strain


title: sRNA - Tet2 KO - exp2 rep2

description:
tRF.counts.tsv.gz
KO.sRNA.e2b2

tag: genotype


title: sRNA - E14 - exp2 rep3

description:
tRF.counts.tsv.gz
E14.sRNA.e2b3


title: sRNA - E14 - exp2 rep2

description:
tRF.counts.tsv.gz
E14.sRNA.e2b2


title: sRNA - Tet2 KO - exp1 rep2

description:
tRF.counts.tsv.gz
KO.sRNA.e1b2

extract_protocol:
Trizol, TBE urea PAGE size selection 14-38 nt
Illumina Truseq small RNA


title: sRNA - WT - exp1 rep3

description:
tRF.counts.tsv.gz
WT.sRNA.e1b3

value: WT


title: sRNA - E14 - exp2 rep1

description:
tRF.counts.tsv.gz
E14.sRNA.e2b1


title: sRNA - WT - exp1 rep2

description:
tRF.counts.tsv.gz
WT.sRNA.e1b2


title: sRNA - Tet2 KO - exp1 rep3

description:
tRF.counts.tsv.gz
KO.sRNA.e1b3


title: sRNA - Tet2 KO - exp1 rep1

description:
tRF.counts.tsv.gz
KO.sRNA.e1b1


title: sRNA - WT - exp1 rep1

description:
tRF.counts.tsv.gz
WT.sRNA.e1b1


title: RNA_WT_P14_Cl13_D20_Terminally_exhausted_2


title: Post_22.026 (RS-02948633)


title: hm5C RIP - rep2

description:
processed data file: RIP.tsv.gz
170924.HJWHVBGX3.RPI18.R2
190627_HeBonasio_sample12

source_name: mESCs_hm5C RIP

extract_protocol:
TRIzol (after IP)
Illumina Truseq sRNA library prep

value: mESCs

value: hm5C RIP


title: TET2 CLIP - clone 75 - rep1

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.H022
190627_HeBonasio_sample7

data_processing:
library strategy: CLIP-seq
CLIP: AdapterRemoval (adapter sequence removal); UMI-tools (de-duplicate using UMI); STAR v 2.5.3a (alignment); DEGseq (map to gene models).
RIP: AdapterRemoval (adapter sequence removal); STAR v 2.5.3a (alignment); DEGseq (map to gene models).
small RNA: cutadapt (adapter sequence removal); fastx toolkit (quality filter; collapse reads to generate read counts); note: 3' tRNA-derived fragments do not align against genomic tRNAs without clipping CCA-tail (use bowtie2-2.2.6 or higher for correct random alignment of multimapping reads)
Genome_build: mm10
Supplementary_files_format_and_content: We provide tab-separated (tsv) count tables for each separate experiment (CLIP, RIP, sRNA-seq)

source_name: mESCs_TET2 CLIP - clone 75

extract_protocol:
CLIP lysis buffer: 10 mM HEPES pH 8.0, 350 mM KCl, 0.5% IGEPAL CA-630
custom eCLIP

value: E14; Tet2HA-His

value: TET2 CLIP


title: RIP input - rep1

description:
processed data file: RIP.tsv.gz
170924.HJWHVBGX3.RPI13.R2
190627_HeBonasio_sample9

source_name: mESCs_RIP input

extract_protocol:
TRIzol
Illumina Truseq sRNA library prep


title: hm5C RIP - rep1

description:
processed data file: RIP.tsv.gz
170924.HJWHVBGX3.RPI17.R2
190627_HeBonasio_sample11


title: RIP input - rep2

description:
processed data file: RIP.tsv.gz
170924.HJWHVBGX3.RPI14.R2
190627_HeBonasio_sample10


title: CLIP input - clone 75 - rep2

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.H035
190627_HeBonasio_sample6

source_name: mESCs_CLIP input - clone 75


title: TET2 CLIP - clone 75 - rep2

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.H048
190627_HeBonasio_sample8


title: TET2 CLIP - clone 65 - rep2

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.ND64
190627_HeBonasio_sample4

source_name: mESCs_TET2 CLIP - clone 65


title: CLIP input - clone 75 - rep1

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.H009
190627_HeBonasio_sample5


title: TET2 CLIP - clone 65 - rep1

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.ND46
190627_HeBonasio_sample3


title: CLIP input - clone 65 - rep1

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.ND37
190627_HeBonasio_sample1

source_name: mESCs_CLIP input - clone 65


title: CreERT2-GFP-3

status: Public on Oct 13 2020

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

description: Bone marrow cells from 7 weeks old mice were harvested and primed with 10 ng ml-1 recombinant mouse IL-7. Pten -/- pre-B cells were further transformed with BCR-ABL1 in the absence of IL-7.

data_processing:
Raw sequence reads were mapped to the mouse genome (mm10) using STAR v2.5.39, and the frequency of genes was counted using featureCounts v1.5.110. The raw counts were then normalized to reads per kilo base per million (RPKM) mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: csv file of RPKM values

source_name: Pten-/- pre B cells transformed with BCR-ABL1 oncogene

growth_protocol: Pten+/+ or Pten-/- bone marrow cells from 7 weeks old mice were harvested by flushing cavities of femur and tibia with chilled PBS followed by filtering through 40 μm strainer to yield a single-cell suspension. Filtered cells were further incubated with lysis buffer (RBC Lysis Buffer, BioLegend) to lyse erythrocytes. After washing with PBS, cells were subjected to further experiments. For IL-7-dependent pre-B cell culture, bone marrow cells were harvested and cultured in Iscove’s modified Dulbecco’s medium (IMDM; GIBCO) with GlutaMAX containing 20% FBS, 50 μM 2-mercaptoethanol, 100 IU ml-1 penicillin, 100 μg ml-1 streptomycin in the presence of 10 ng ml-1 recombinant mouse IL-7 (Peprotech). pre-B cells were retrovirally transformed by BCR-ABL1 and then IL-7 was removed to select the transduced cells.

extract_protocol:
Total mRNA was extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions.
Libraries were constructed using the TruSeq PE Cluster Kit V4-cBot-HS (Illumina®).

tag: hematopoietic malignancy

value: Pre-B ALL, BCR-ABL1

value: Pten-/-

value: pre B cells


title: HCT116_Input_3

status: Public on Nov 03 2020

city: Houston

first: Sankar

last: Mitra

state: Texas

address: 6445 Main Street

department: Houston Methodist Cancer Center

institute: Houston Methodist Resrarch Institute

description: input DNA before ChIP

data_processing:
Fastq files were preprocessed with the Trim Galore wrapper (trim_galore --fastqc --length 20 --paired run1, run2) for adapter trimming (cutadapt) and reads quality control (FastQC). On average, 1.9 ± 1.6% (mean ± SD) sequence pairs were discarded because their length was below the threshold and 37,345,085 ± 2,279,420 (values are given as mean ± SD unless otherwise specified) reads passed the filters.
Trimmed reads were mapped to both GRCh37/hg19 and GRCh38/hg38 human genome assemblies with Bowtie2 using the -q --very-sensitive parameter. The overall alignment rate was ~1-2% higher for the hg38 than for the hg19 assembly. The alignment rate for IgG, 47.0 ± 6.0%, was low compared to Input (98.4 ± 0.1%) and AcNEIL1 (98.0 ± 0.9%). Thus, Input was used as control.
Sorted bam files and bam indices were obtained with samtools. Sorted bam files were processed with “bedtools intersect” to filter out a blacklist (file wgEncodeDacMapabilityConsensusExcludable.bed.gz from (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/ lifted to hg38 coordinates for the hg38 mapping) of genomic regions identified by the ENCODE consortium as yielding artifactually high signals.
The utilities “macs2 filterdup” and “macs2 predictd” were then used to remove duplicates and to extract fragment length to build a shifting model for peak detection.
Narrow peaks were called with “macs2 callpeak” using both a Poisson-distributed shifting model or a “noModel” process with the fragment length obtained from the “predictd” parameter. The average number of peaks obtained from the two methods was similar (49608 ± 10741 for noModel and 49955 ± 10169 for model for hg38; p = NS). Therefore, we chose the peak collection from the model for subsequent analyses. ChIPQC was used to assess the quality of called peaks.
Genome_build: hg38
Supplementary_files_format_and_content: To visualize the AcNEIL1 ChIP-seq data on the UCSC browser, we used macs2 with the “bdgcmp” option to generate fold enrichment (FE) and logLR peak enrichment files in bedGraph format, which were then transformed into BigWig format with the bedtools “slop” option, followed by sorting with bedClip and the UCSC utility bedGraphToBigWig.

source_name: HCT116 (ATCC # CCL-247)

growth_protocol: The human colorectal adenocarcinoma HCT116 (ATCC # CCL-247) cell line was grown in McCoy’s 5A medium (Gibco/Life Technologies) containing 10% fetal calf serum (FCS; Sigma) and an antibiotic mixture of 100 IU penicillin and 100 µg/mL streptomycin (Corning) at 37 °C under 5% CO2 and 95% relative humidity. Cells were grown in 10-15 10-cm dishes for each ChIP-Seq experiment.

extract_protocol:
ChIP assays. A) Direct ChIP assays. ChIP assays were performed on exponentially growing cells (one 70-80%-confluent 10-cm plate for one ChIP reaction) with Magna ChIP Protein A/G magnetic beads (Millipore, # 16-663) using the custom-generated rabbit α-AcNEIL1, rabbit α-H3K27Ac (Cell Signaling; 8173) antibodies or control IgG as described below. After washing in phosphate buffered saline (PBS), cells were crosslinked with 1% formaldehyde (15 min at room temperature) in PBS. Crosslinked cells were washed three times in PBS and scraped off the plates in PBS containing a protease inhibitor (PI) cocktail (Thermo Scientific/Pierce; # 88666) and pelleted at 900 RPM (10 min, 4 ºC). Pelleted cells were lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8, PI), incubated on ice for 10 min and subjected to sonication (XL-2000 QSonica LLC) on ice by setting the pulse at 4 for 4-5 times with a 1 min interval in between, followed by centrifugation (14,000 RPM, 15 min, 4 ºC) to collect the sheared chromatin lysate. IP was performed in this chromatin lysate with 30 µL Protein A/G magnetic beads, the corresponding antibody (5 µg; control IgG was included in a separate IP) in a total volume of 2 mL (diluted 1:10 with ChIP dilution buffer: 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, PI) overnight (4 ºC) with constant shaking. The next day, the IPs were washed sequentially with low salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8, 150 mM NaCl), high salt immune complex wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8, 500 mM NaCl), LiCl immune complex wash buffer (0.25 M LiCl, 1% NP40, 1% Na-deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8) and TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). The protein-DNA complexes were eluted in ChIP elution buffer (1% SDS, 0.1 M NaHCO3), de-crosslinked in 200 mM NaCl for 4 h at 65 ºC. ChIP DNA was purified by proteinase K digestion, RNAse treatment, phenol chloroform extraction and ethanol precipitation using standard protocols. The ChIP-purified DNA was finally dissolved in 10 mM Tris-Cl pH 8. The ChIP and 10% input DNA were subjected to SYBR GREEN-based qPCR (7500 Real-Time PCR System; Applied Biosystems) with primers (Table S2) and SYBR Premix Ex Taq (TaKaRa). Data were represented as % input according to http://www.lifetechnologies.com/us/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip/chip-analysis.html.  B) ChIP-seq assays. For ChIP-seq assays, the direct ChIP protocol above was followed with the following modifications: about 70%-confluent exponentially growing HCT116 cells in 10-cm plates (10-15 plates) were pelleted after crosslinking and PBS wash. Hypotonic lysis buffer (20 mM HEPES pH 7.9. 10 mM KCl, 1 mM EDTA, 10% glycerol, 1 mM DTT, PI) was added to the cell pellet, followed by incubation on ice for 15 min. Cells were then centrifuged at 900 RPM (10 min, 4 ºC), and RIPA buffer (10 mM Tris-Cl pH 8, 140 mM NaCl, 1% Triton-X 100, 0.1% SDS, 1% sodium deoxycholate, 1 mM DTT, PI) was added to the pellet, incubated on ice for 10 min to extract the nuclear lysate, which was sonicated 12 times. IP was carried out in the sheared chromatin lysate with 80 µL protein A/G magnetic beads, the corresponding antibody (10 µg; control IgG was included in a separate IP) in a total volume of 3-4 mL (diluted with ChIP dilution buffer) overnight at 4 ºC with constant shaking. Next day, the IPs were washed three times with RIPA buffer, then with PBS and finally with TE buffer. The protein-DNA complexes were eluted in ChIP elution buffer, de-crosslinked and finally the ChIP-ed DNA was purified by proteinase K digestion, RNAse treatment, phenol chloroform extraction and ethanol precipitation. The ChIP-purified DNA was finally dissolved in 10 mM Tris-Cl pH 8 and subjected to NSG.  on an Illumina HiSeq 4000 sequencer performing a 76nt paired-end sequencing read format. ChIP DNA was quantified by Nanodrop Spectrophotometer and then used to create an NGS library following the TruSeq v2 (Illumina) protocol.
ChIP sequencing was performed in the Advanced Technology Genomics Core (ATGC) Facility at MD Anderson Cancer Center. Briefly, Illumina compatible indexed libraries were prepared from 10 - 20 ng of Diagenode Biorupter Pico sheared ChIP DNA using the KAPA Hyper Library Preparation Kit (KAPA Biosystems, Inc.). Libraries were amplified by 15 cycles of PCR, then assessed for size distribution using the 4200 TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher.). Equimolar quantities of the indexed libraries were multiplexed, 9 libraries per pool. The pool was quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) then sequenced in one lane of the Illumina HiSeq4000 sequencer using the 76nt paired-end run format. Triplicate samples were subjected to NGS for AcNEIL1, Input and IgG controls.

treatment_protocol: Cells were sub-cultured the day before harvesting, and exponentially growing cells were processed for crosslinking and harvesting as detailed below.

tag: cell line origin

value: human colorectal adenocarcinoma

tag: chip antibody

tag: sample

value: input DNA before ChIP


title: CreERT2-GFP-2


title: HCT116_AcNEIL1_2

description: ChIP purified DNA

value: rabbit α-AcNEIL1 antibody (Sengupta S 2018, DNA Repair 66-67:1-10)

value: ChIP purified DNA


title: HCT116_AcNEIL1_1

description: ChIP purified DNA


title: HCT116_Input_2

description: input DNA before ChIP


title: HCT116_AcNEIL1_3

description: ChIP purified DNA


title: ERT2-GFP-3

description: Bone marrow cells from 7 weeks old mice were harvested and primed with 10 ng ml-1 recombinant mouse IL-7. Pten +/+ pre-B cells were further transformed with BCR-ABL1 in the absence of IL-7.

source_name: Pten+/+ pre B cells transformed with BCR-ABL1 oncogene

value: Pten+/+


title: CreERT2-GFP-1


title: ERT2-GFP-2


title: ERT2-GFP-1


title: NRAS-G12D-Ifitm3-KO-3

description: Bone marrow cells from 7 weeks old mice were harvested and primed with 10 ng ml-1 recombinant mouse IL-7. Ifitm3 -/- pre-B cells were further transformed with NRAS-G12D in the presence of IL-7.

data_processing:
Transcript were quantified using Salmon v1.1.0 against gencode GRCm38 vM24 transcript annotations.
Differential expression and normalisation was done in R using DESeq2 v1.28.1.
Genome_build: mm10
Supplementary_files_format_and_content: csv files of DESeq2 results and rlog normalised expression values for each oncogene

source_name: Ifitm3-/- pre B cells transformed with NRAS-G12D oncogene

growth_protocol: Ifitm3+/+ or Ifitm3-/- bone marrow cells from 7 weeks old mice were harvested by flushing cavities of femur and tibia with chilled PBS followed by filtering through 40 μm strainer to yield a single-cell suspension. Filtered cells were further incubated with lysis buffer (RBC Lysis Buffer, BioLegend) to lyse erythrocytes. After washing with PBS, cells were subjected to further experiments. For IL-7-dependent pre-B cell culture, bone marrow cells were harvested and cultured in Iscove’s modified Dulbecco’s medium (IMDM; GIBCO) with GlutaMAX containing 20% FBS, 50 μM 2-mercaptoethanol, 100 IU ml-1 penicillin, 100 μg ml-1 streptomycin in the presence of 10 ng ml-1 recombinant mouse IL-7 (Peprotech). For BCR–ABL1 leukemia model, pre-B cells were retrovirally transformed by BCR-ABL1 and then IL-7 was removed to select the transduced cells. NrasG12D ALL cells were selected with puromycin (GIBCO) and were maintained with IL-7 added IMDM.  Total mRNA from Ifitm3+/+ and Ifitm3-/- BCR-ABL1 or NRASG12D B-ALL cells was extracted using RNeasy Kit (Qiagen) according to the manufacturer’s instructions. Sequencing was performed on an Illumina Hiseq 2500 (Illumina, San Diego, CA, USA) instrument using the TruSeq PE Cluster Kit V4-cBot-HS (Illumina®) to generate 101 bp Paired-end reads sequencing with v4 chemistry. Quality control of RNA-Seq reads was performed using FastQC.

value: Pre-B ALL, NRAS-G12D

tag: transformed with


title: NRAS-G12D-Ifitm3-KO-2


title: NRAS-G12D-Ifitm3-KO-1


title: BCR-ABL1-Ifitm3-KO-3

description: Bone marrow cells from 7 weeks old mice were harvested and primed with 10 ng ml-1 recombinant mouse IL-7. Ifitm3 -/- pre-B cells were further transformed with BCR-ABL1 in the absence of IL-7.

source_name: Ifitm3-/- pre B cells transformed with BCR-ABL1 oncogene


title: BCR-ABL1-Ifitm3-KO-1


title: NRAS-G12D-WT-2

description: Bone marrow cells from 7 weeks old mice were harvested and primed with 10 ng ml-1 recombinant mouse IL-7. Ifitm3 +/+ pre-B cells were further transformed with NRAS-G12D in the presence of IL-7.

source_name: Ifitm3+/+ pre B cells transformed with NRAS-G12D oncogene


title: CLIP input - clone 65 - rep2

description:
processed data file: CLIP.tsv.gz
170820.H5TGTBGX3.ND55
190627_HeBonasio_sample2


title: BCR-ABL1-Ifitm3-KO-2


title: BCR-ABL1-WT-2

description: Bone marrow cells from 7 weeks old mice were harvested and primed with 10 ng ml-1 recombinant mouse IL-7. Ifitm3 +/+ pre-B cells were further transformed with BCR-ABL1 in the absence of IL-7.

source_name: Ifitm3+/+ pre B cells transformed with BCR-ABL1 oncogene


title: NRAS-G12D-WT-1


title: NRAS-G12D-WT-3


title: BCR-ABL1-WT-1


title: HCT116_Input_1

description: input DNA before ChIP


title: Old fly brain - rep 4

status: Public on Aug 17 2020

data_processing:
RNA-seq reads were mapped to the Drosophila melanogaster assembly BDGP6 pre-indexed with transcript models from Ensembl 87 using STAR 2.5.0b with default parameters except --alignIntronMax set to 10,000
Aligned reads were assigned to gene models using the summarizeOverlaps function of the GenomicRanges R package
Reads per kilobase per million (RPKMs) were calculated with a slight modification, whereby only reads assigned to annotated protein-coding genes were used in the denominator, to minimize batch variability due to different amounts of contaminant ribosomal RNA
Genome_build: BDGP6
Supplementary_files_format_and_content: count table

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: y1w* flies were raised at 25˚C and 50% humidity on a 12-hour light–dark cycle using standard Bloomington Drosophila Medium (Nutri-Fly)

extract_protocol:
After 5 days (young) and 70 days (old), brains were dissected and RNA was purified with TRIzol.
PolyA+ RNA was purified using Dynabeads Oligo(dT)25 (Thermo Fisher) beads and constructed into strand-specific libraries using the dUTP method . UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics, MA), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual-indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter, CA) and quantified by qPCR before and after amplification. Sequencing was performed in paired-end mode on a NextSeq 500 (Illumina, CA).

tag: tissue

value: Brain

tag: age

value: 70 days

tag: internal name


title: M3

status: Public on Sep 11 2020

city: San Diego

first: Tariq

last: Rana

state: CA

address: 9500 Gilman Dr

department: Paediatrics

institute: UCSD

data_processing:
demultiplexing based on illumina indexing sequences
Filtering and alignment to GRCh38.p11 were performed using the 10x Genomics Cell Ranger 2.0.0 pipeline following standard parameters
Genome_build: GRCh38.p11
Supplementary_files_format_and_content: .mtx sparse matrix for gene expresson and .tsv files for single cell barcodes and gene names

source_name: hESC derived cerebral organoid

growth_protocol: cerebral organoids were generated using the intrinsic approach developed by Lancaster et al. Briefly, embyroid bodies were generated from h9 human embyronic stem cells were using microwell plates or hanging drop method and differentiated into neural and glial lineages with retinoic acid, insulin, B27 and N2 in suspension culture within spinner flasks.

extract_protocol:
RNAs were extracted from single cells using the 10x Genomics Chromium controller to generate gel bead emulsions.
scRNA-seq libraries were generated following the 10x Genomics V2 scRNA-seq protocol.

treatment_protocol: Cerebral organoids were treated with 5uM methamphetamine for 7 days before being analyzed by scRNA-seq.

tag: cell type

value: hESC derived cerebral organoid

tag: treatment

value: 5uM Methamphetamine


title: M2


title: Old fly brain - rep 3


title: Young fly brain - rep3

value: 5 days


title: Old fly brain - rep 1


title: Young fly brain - rep1


title: Young fly brain - rep2


title: BCR-ABL1-WT-3

value: WT


title: Injury day 3 - rep4

data_processing:
Sequencing files from both 10x Genomics and Drop-seq experiments were processed using Drop-seq tools v2.0.0, developed by the McCarroll Lab (https://github.com/broadinstitute/Drop-seq).
Sequencing data were aligned to a combined reference of the current Harpegnathos saltator assembly (Hsal_v8.5) and the Drosophila melanogaster genome assembly (assembly Release 6 plus ISO1 MIT).
Reads mapping to features from the Harpegnathos annotation (Hsal_v8.5) were counted and a UMI matrix was produced for all cells with a minimum number of 150 genes.
Genome_build: Hsal_v8.5 and Drosophila melanogaster release 6 plus ISO1 MIT
Supplementary_files_format_and_content: digital expression (DGE) matrix

organism: Harpegnathos saltator

source_name: non-visual brain

growth_protocol: Animals were housed in a plaster nest in a clean, temperature  (25°C) and humidity (50%) controlled ant facility on a 12-hour light/dark cycle and fed three times per week with live crickets.

extract_protocol:
Brains were removed from ants and optic lobes were removed in DMEM medium, then washed twice with DMEM medium. 1 mL of papain solution (5 mL DMEM medium/vial with 45 uM actinomycin D) was added and brains were rotated at room temperature for 12 minutes. Following two washes with DMEM medium and one wash with PBS solution (1x PBS with 0.01% BSA), brains were resuspended in 200 µL PBS solution, pipetting up and down. Samples were incubated for 5 minutes and pipetting was repeated. Samples were filtered with a 40 µm strainer to obtain a single-cell suspension.
For 10x sequencing, cells were loaded to RT mix to aim for sampling of 5,000–10,000 cells. All downstream cDNA synthesis (12 PCR cycles), library preparation, and sequencing were carried out as instructed by the manufacturer (10x Genomics Chromium Single Cell 3' Reagent Kit v2 User Guide RevD) with minor modifications; custom barcodes were used as indexes, libraries were loaded at 2.0 pM, and the read configuration was 26 bp (read 1), 8 bp (index 1), and 58 bp (read 2). For Drop-seq, the final cell suspension was diluted to 100 cells/µL with PBS solution and 1.5 mL of the cell suspension was loaded for each Drop-seq run. Barcoded beads were resuspended in freshly made lysis buffer, composed of 200 mM Tris-HCl (pH 8.0 at room temperature), 20 mM EDTA, 6% Ficoll PM-400 (GE Healthcare/Fisher Scientific), 0.2% sarkosyl (Sigma Aldrich), and 50 mM DTT, at a concentration of 120 beads/mL. The flow rate for cells and beads were set to 4,000 mL/h, while droplet generation oil (Bio-rad) was run at 15,000 mL/h. Droplets were generated and collected in a 50 mL Falcon tube for a run time of 15 minutes. Droplet breakage with Perfluoro-1-octanol (Sigma-Aldrich), reverse transcription, exonuclease I treatment, and amplification of cDNA were performed following the Drop-seq protocol of the McCarroll lab (http://mccarrolllab.org/dropseq/), with minor modifications. cDNA was amplified using Terra PCR Direct Polymerase Mix Kit. After two rounds of purification with 0.6x SPRISelect beads, we tagmented 600 pg DNA using the Nextera XT DNA Sample Preparation Kit (Illumina, cat # FC-131-1096). Libraries were further amplified with 12 PCR cycles using custom P5-TSO hybrid and custom Nextera-compatible primers with different indexes. Libraries were loaded at 2.0 pM. Custom read 1 and index 2 primers were used, and libraries were sequenced on an Illumina NextSeq500 using a 75-cycle High Output v2 Kit (Illumina, cat # FC-404-2005). The read configuration was 20 bp (read 1), 8 bp (index 1), 8bp (index 2), and 56 bp (read 2).

tag: technology

value: Drop-seq

tag: caste

value: worker

value: brain (minus optic lobes)

tag: colony type

value: stable colony

value: injury


title: Injury day 3 - rep3


title: Mock day 3 - rep1

value: mock


title: Mock day 3 - rep3


title: Mock day 3 - rep2


title: Injury day 1 - rep2


title: Day 120 aging - gamergate - rep2

value: gamergate


title: Injury day 1 - rep1


title: Day 120 aging - gamergate - rep1


title: Mock day 1 - rep3


title: Day 120 aging - gamergate - rep3


title: Mock day 1 - rep2


title: Day 120 aging - worker - rep4


title: Day 120 aging - worker - rep1


title: Day 120 aging - worker - rep2


title: Old fly brain - rep 2


title: Injury day 3 - rep2


title: Injury day 3 - rep1


title: Day 30 aging - worker - rep3


title: Day 30 aging - worker - rep2


title: Day 120 aging - worker - rep3


title: Injury day 1 - rep3


title: RNAseq - MTF2-AID ESCs day 0 - untreated - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0611
MAID.NT.ESC.b2

source_name: ESCs

value: MTF2-AID, Tir1

value: untreated

tag: length of treatment

value: 12 hours


title: Day 30 aging - worker - rep1


title: Day 120 aging - worker - rep5


title: Mock day 1 - rep1


title: Day 5 aging - worker - rep1


title: Day 5 aging - worker - rep2


title: Day 90 aging - worker - rep3


title: Day 5 aging - worker - rep3


title: Day 90 aging - worker - rep2


title: Day 90 aging - worker - rep1


title: Day 30 transition - worker - rep6

value: 10x Genomics

value: transition


title: Day 30 transition - gamergate - rep4


title: Day 30 transition - worker - rep4


title: Day 30 transition - worker - rep2


title: Day 30 transition - gamergate - rep3


title: Day 30 transition - gamergate - rep


title: Day 30 transition - worker - rep3


title: Day 5 aging - worker - rep4


title: Control

status: Public on Jun 17 2020

city: Moscow

first: Dmitry

middle: Vadimovich

last: Bikmetov

state: Moscow

address: Vavilova, 34/5

country: Russia

institute: Center for Precision Genome Editing and Genetic Technologies for Biomedicine, IGB RAS

data_processing:
The raw reads were trimmed and quality filtered with Skewer 0.2.2
Reads mapped to rRNA and tRNA sequences were discarded. Mapping was performed using Bowtie 1.2.2, allowing no more than two mismatches.
Remaining reads were uniquely mapped to the E. coli MG1655 genome with the same program and parameters.
Reads shorter than 15 nt or longer than 40 nt were excluded.
Ribosome density (occupancy) was calculated as the number of 3’-ends of footprints normalized by the total number of uniquely mapped reads (in millions).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Separate wig files for each strand containing ribosome density (occupancy).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Cell culture

growth_protocol: The overnight cultures of E. coli BW25113 cells transformed with pBAD33 bearing a toxin gene or an empty pBAD33 vector were diluted 200-fold into 200 ml of MOPS medium supplemented with 33 μg/ml chloramphenicol and 1% glucose and were grown at 37°C with vigorous shaking to an OD600 of 0.2.

extract_protocol:
The cells were harvested and lyzed as described in Becker et al. 2013. The cellular lysates were clarified by centrifugation at 20,000 x g at 4°C for 10 min. The lysates were diluted with the lysis buffer  to adjust the OD260 to 0.1 in the final volume of 220 μl and treated with ~450 U of MNase (Roche) at 25°C for 1 hr. The reaction was quenched by the addition of EGTA to the final concertation of 5 mM. The monosomal material was purified by sucrose gradient centrifugation. RNA was purified as described in Becker et al. 2013.
Libraries were constructed as described in Becker et al. 2013

treatment_protocol: The cells were pelleted and resuspended in fresh MOPS medium supplemented with 33 μg/ml chloramphenicol without glucose and grown at 37°C for 30 min, followed by 15 min induction with 1 mM arabinose.

tag: strain background

tag: genotype/variation

tag: time point

value: 15 min after induction


title: Day 30 transition - worker - rep1


title: Day 30 transition - gamergate - rep1


title: Donor_313C_HSCMPP_BM_835

status: Public on Jan 14 2020

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
RNA-seq reads were aligned to GRCh38 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.6.0) with the parameter (-s no).
Genome_build: GRCh38
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

source_name: Bone marrow

extract_protocol:
HSC/MPPs were purified by flow cytometry sorting from CD34+ enriched (magnetic selection) bone marrow or spleen samples as CD19- CD34+ CD38- CD45RA-. Single cell were directly sorted into lysis buffer according to the Smart-seq2 protocol published by Picelli et al., Nat. Protocol 2014.
RNA libraries were prepared for sequencing using standard SmartSeq2 protocols and the Illumina Nextera XD DNA sample preparation protocol.

tag: donor

value: Donor 2 (313C)

value: 35 years old

tag: gender

value: female

tag: organ donation death type

value: Donation after circulatory death (DCD)

value: Bone marrow

value: single HSC or MPP

tag: cell id


title: Donor_313C_HSCMPP_BM_836


title: AtaT2


title: Day 30 transition - gamergate - rep5

value: brain (minus optic lobes)


title: Donor_313C_HSCMPP_BM_833


title: Donor_313C_HSCMPP_BM_834


title: Donor_313C_HSCMPP_BM_832


title: Donor_313C_HSCMPP_BM_829


title: Donor_313C_HSCMPP_BM_830


title: Donor_313C_HSCMPP_BM_827


title: Donor_313C_HSCMPP_BM_826


title: Day 30 transition - worker - rep5

value: worker


title: Donor_313C_HSCMPP_BM_825


title: Donor_313C_HSCMPP_BM_824


title: Donor_313C_HSCMPP_BM_823


title: Donor_313C_HSCMPP_BM_821


title: Donor_313C_HSCMPP_BM_820


title: Donor_313C_HSCMPP_BM_818


title: Donor_313C_HSCMPP_BM_819


title: Donor_313C_HSCMPP_BM_822


title: Donor_313C_HSCMPP_BM_831


title: Donor_313C_HSCMPP_BM_813


title: Donor_313C_HSCMPP_BM_828


title: Donor_313C_HSCMPP_BM_808


title: Donor_313C_HSCMPP_BM_812


title: Donor_313C_HSCMPP_BM_814


title: Donor_313C_HSCMPP_BM_815


title: Donor_313C_HSCMPP_BM_809


title: Donor_313C_HSCMPP_BM_811


title: Donor_313C_HSCMPP_BM_804


title: Donor_313C_HSCMPP_BM_803


title: Donor_313C_HSCMPP_BM_807


title: Donor_313C_HSCMPP_BM_802


title: Donor_313C_HSCMPP_BM_805


title: Donor_313C_HSCMPP_BM_806


title: Donor_313C_HSCMPP_BM_800


title: Donor_313C_HSCMPP_BM_799


title: Donor_313C_HSCMPP_BM_817


title: Donor_313C_HSCMPP_BM_797


title: Donor_313C_HSCMPP_BM_816


title: Donor_313C_HSCMPP_BM_796


title: Donor_313C_HSCMPP_BM_792


title: Donor_313C_HSCMPP_BM_793


title: Donor_313C_HSCMPP_BM_801


title: Donor_313C_HSCMPP_BM_795


title: Donor_313C_HSCMPP_BM_790


title: Donor_313C_HSCMPP_BM_791


title: Donor_313C_HSCMPP_BM_794


title: Donor_313C_HSCMPP_BM_782


title: Donor_313C_HSCMPP_BM_783


title: Donor_313C_HSCMPP_PB_778

source_name: Periferal blood

value: Periferal blood


title: Donor_313C_HSCMPP_BM_786


title: Donor_313C_HSCMPP_PB_789


title: Donor_313C_HSCMPP_PB_787


title: Donor_313C_HSCMPP_PB_777


title: Donor_313C_HSCMPP_BM_810


title: Donor_313C_HSCMPP_BM_798


title: Donor_313C_HSCMPP_PB_788


title: Donor_313C_HSCMPP_BM_781


title: Donor_313C_HSCMPP_BM_773


title: Donor_313C_HSCMPP_BM_772


title: Donor_313C_HSCMPP_BM_785


title: Donor_313C_HSCMPP_BM_771


title: Donor_313C_HSCMPP_BM_774


title: Donor_313C_HSCMPP_BM_779


title: RNAseq - SUZ12-AID ESCs day 0 - auxin - rep2

description:
all.ESC.NPC.TPMs.tsv.gz
190622.HYG22BGX9.b0608
S12AID.IAA.ESC.b2

extract_protocol:
Cells were rinsed once with PBS and lysed via direct addition of TRIzol reagent (Thermo Fisher Scientific). Total cellular RNA was purified using the Direct-zol RNA Miniprep kit (Zymo Research).
PolyA+ RNA was isolated from 500 ng total RNA using Dynabeads Oligo(dT)25 beads (Thermo Fisher) and constructed into strand-specific libraries using the dUTP method. UTP-marked cDNA was end-repaired using end-repair mix (Enzymatics), tailed with deoxyadenine using Klenow exo- (Enzymatics), and ligated to custom dual indexed adapters with T4 DNA ligase (Enzymatics). Libraries were size-selected with SPRIselect beads (Beckman Coulter) and quantified by qPCR before and after amplification.

tag: strain

tag: genotype

value: SUZ12-AID, Tir1

value: auxin


title: Donor_313C_HSCMPP_BM_784

tag: age

tag: tissue


title: Donor_313C_HSCMPP_PB_767

tag: cell type


title: Donor_313C_HSCMPP_BM_775


title: Donor_313C_HSCMPP_BM_780


title: Donor_313C_HSCMPP_BM_768


title: Donor_313C_HSCMPP_BM_769


title: Donor_313C_HSCMPP_BM_770


title: Donor_313C_HSCMPP_PB_765


title: Donor_313C_HSCMPP_PB_776


title: Donor_313C_HSCMPP_BM_764


title: Donor_313C_HSCMPP_BM_762


title: Donor_313C_HSCMPP_BM_761


title: Donor_313C_HSCMPP_BM_763


title: Donor_313C_HSCMPP_BM_758


title: Donor_313C_HSCMPP_PB_755


title: Donor_313C_HSCMPP_BM_757


title: Donor_313C_HSCMPP_BM_760


title: Donor_313C_HSCMPP_PB_756


title: Donor_313C_HSCMPP_BM_759


title: Donor_313C_HSCMPP_BM_751


title: Donor_313C_HSCMPP_BM_748


title: Donor_313C_HSCMPP_BM_750


title: Donor_313C_HSCMPP_PB_754


title: Donor_313C_HSCMPP_SPL_744

source_name: Spleen

value: Spleen


title: Donor_313C_HSCMPP_SPL_746


title: Donor_313C_HSCMPP_BM_753


title: Donor_313C_HSCMPP_BM_747


title: Donor_313C_HSCMPP_BM_752


title: Donor_313C_HSCMPP_SPL_745


title: Donor_313C_HSCMPP_BM_742


title: Donor_313C_HSCMPP_BM_743


title: Donor_313C_HSCMPP_BM_741


title: Donor_313C_HSCMPP_BM_749


title: Donor_313C_HSCMPP_BM_739


title: Donor_313C_HSCMPP_PB_766


title: Donor_313C_HSCMPP_BM_737


title: Donor_313C_HSCMPP_SPL_736


title: Donor_313C_HSCMPP_BM_738


title: Donor_313C_HSCMPP_SPL_734


title: Donor_313C_HSCMPP_BM_733


title: Donor_313C_HSCMPP_SPL_735


title: Donor_313C_HSCMPP_BM_731


title: Donor_313C_HSCMPP_BM_729


title: Donor_313C_HSCMPP_BM_730


title: Donor_313C_HSCMPP_BM_727


title: Donor_313C_HSCMPP_BM_732


title: Donor_313C_HSCMPP_BM_728


title: Donor_313C_HSCMPP_BM_740


title: Donor_313C_HSCMPP_SPL_724


title: Donor_313C_HSCMPP_SPL_726


title: Donor_313C_HSCMPP_BM_722


title: Donor_313C_HSCMPP_SPL_725


title: Donor_313C_HSCMPP_BM_720


title: Donor_313C_HSCMPP_BM_718


title: Donor_313C_HSCMPP_SPL_716


title: Donor_313C_HSCMPP_SPL_714


title: Donor_313C_HSCMPP_SPL_715


title: Donor_313C_HSCMPP_BM_712


title: Donor_313C_HSCMPP_BM_711


title: Donor_313C_HSCMPP_BM_719


title: Donor_313C_HSCMPP_BM_717


title: Donor_313C_HSCMPP_BM_721


title: Donor_313C_HSCMPP_BM_713


title: Donor_313C_HSCMPP_BM_709


title: Donor_313C_HSCMPP_BM_710


title: Donor_313C_HSCMPP_BM_708


title: Donor_313C_HSCMPP_BM_707


title: Donor_313C_HSCMPP_BM_705


title: Donor_313C_HSCMPP_BM_706


title: Donor_313C_HSCMPP_BM_723


title: Donor_313C_HSCMPP_BM_701


title: Donor_313C_HSCMPP_BM_702


title: Donor_313C_HSCMPP_BM_703


title: Donor_313C_HSCMPP_BM_697


title: Donor_313C_HSCMPP_BM_704


title: Donor_313C_HSCMPP_BM_696


title: Donor_313C_HSCMPP_BM_698


title: Donor_313C_HSCMPP_BM_699


title: Donor_313C_HSCMPP_BM_693


title: Donor_313C_HSCMPP_BM_694


title: Donor_313C_HSCMPP_BM_692


title: Donor_313C_HSCMPP_BM_691


title: Donor_313C_HSCMPP_BM_685


title: Donor_313C_HSCMPP_BM_684


title: Donor_313C_HSCMPP_BM_686


title: Donor_313C_HSCMPP_BM_689


title: Donor_313C_HSCMPP_BM_690


title: Donor_313C_HSCMPP_BM_687


title: Donor_313C_HSCMPP_BM_700


title: Donor_313C_HSCMPP_BM_695


title: Donor_313C_HSCMPP_PB_677


title: Donor_313C_HSCMPP_PB_681


title: Donor_313C_HSCMPP_BM_683


title: Donor_313C_HSCMPP_PB_679


title: Donor_313C_HSCMPP_PB_675


title: Donor_313C_HSCMPP_PB_680


title: Donor_313C_HSCMPP_PB_682


title: Donor_313C_HSCMPP_PB_678


title: Donor_313C_HSCMPP_PB_674


title: Donor_313C_HSCMPP_PB_676


title: Donor_313C_HSCMPP_PB_670


title: Donor_313C_HSCMPP_PB_673


title: Donor_313C_HSCMPP_BM_688


title: Donor_313C_HSCMPP_PB_667


title: Donor_313C_HSCMPP_PB_666


title: Donor_313C_HSCMPP_PB_665


title: Donor_313C_HSCMPP_PB_664


title: Donor_313C_HSCMPP_PB_671


title: Donor_313C_HSCMPP_PB_660


title: Donor_313C_HSCMPP_PB_669


title: Donor_313C_HSCMPP_PB_672


title: Donor_313C_HSCMPP_PB_668


title: Donor_313C_HSCMPP_PB_662


title: Donor_313C_HSCMPP_PB_661


title: Donor_313C_HSCMPP_PB_657


title: Donor_313C_HSCMPP_PB_663


title: Donor_313C_HSCMPP_PB_658


title: Donor_313C_HSCMPP_PB_656


title: Donor_313C_HSCMPP_PB_654


title: Donor_313C_HSCMPP_PB_651


title: Donor_313C_HSCMPP_PB_655


title: Donor_313C_HSCMPP_SPL_650


title: Donor_313C_HSCMPP_SPL_646


title: Donor_313C_HSCMPP_SPL_649


title: Donor_313C_HSCMPP_SPL_645


title: Donor_313C_HSCMPP_PB_653


title: Donor_313C_HSCMPP_PB_652


title: Donor_313C_HSCMPP_SPL_644


title: Donor_313C_HSCMPP_SPL_647


title: Donor_313C_HSCMPP_SPL_643


title: Donor_313C_HSCMPP_SPL_648


title: Donor_313C_HSCMPP_SPL_640


title: Donor_313C_HSCMPP_SPL_642


title: Donor_313C_HSCMPP_PB_659


title: Donor_313C_HSCMPP_SPL_638


title: Donor_313C_HSCMPP_SPL_639


title: Donor_313C_HSCMPP_SPL_636


title: Donor_313C_HSCMPP_SPL_629


title: Donor_313C_HSCMPP_SPL_628


title: Donor_313C_HSCMPP_SPL_635


title: Donor_313C_HSCMPP_SPL_634


title: Donor_313C_HSCMPP_SPL_630


title: Donor_313C_HSCMPP_SPL_632


title: Donor_313C_HSCMPP_SPL_633


title: Donor_313C_HSCMPP_SPL_631


title: Donor_313C_HSCMPP_SPL_627


title: Donor_313C_HSCMPP_SPL_637


title: Donor_313C_HSCMPP_BM_618


title: Donor_313C_HSCMPP_SPL_622


title: Donor_313C_HSCMPP_BM_617


title: Donor_313C_HSCMPP_SPL_624


title: Donor_313C_HSCMPP_SPL_619


title: Donor_313C_HSCMPP_SPL_641


title: Donor_313C_HSCMPP_SPL_623


title: Donor_313C_HSCMPP_SPL_626


title: Donor_313C_HSCMPP_SPL_625


title: Donor_313C_HSCMPP_BM_611


title: Donor_313C_HSCMPP_SPL_621


title: Donor_313C_HSCMPP_BM_609


title: Donor_313C_HSCMPP_BM_614


title: Donor_313C_HSCMPP_BM_615


title: Donor_313C_HSCMPP_BM_610


title: Donor_313C_HSCMPP_BM_613


title: Donor_313C_HSCMPP_BM_616


title: Donor_313C_HSCMPP_BM_612


title: Donor_313C_HSCMPP_BM_606


title: Donor_313C_HSCMPP_BM_607


title: Donor_313C_HSCMPP_BM_603


title: Donor_313C_HSCMPP_BM_605


title: Donor_313C_HSCMPP_BM_604


title: Donor_313C_HSCMPP_SPL_620


title: Donor_313C_HSCMPP_BM_601


title: Donor_313C_HSCMPP_BM_602


title: Donor_313C_HSCMPP_BM_598


title: Donor_313C_HSCMPP_BM_597


title: Donor_313C_HSCMPP_BM_595


title: Donor_313C_HSCMPP_BM_593


title: Donor_313C_HSCMPP_BM_596


title: Donor_313C_HSCMPP_BM_594


title: Donor_313C_HSCMPP_BM_599


title: Donor_313C_HSCMPP_BM_591


title: Donor_313C_HSCMPP_BM_592


title: Donor_313C_HSCMPP_BM_589


title: Donor_313C_HSCMPP_BM_588


title: Donor_313C_HSCMPP_BM_590


title: Donor_313C_HSCMPP_BM_587


title: Donor_313C_HSCMPP_BM_586


title: Donor_313C_HSCMPP_BM_608


title: Donor_313C_HSCMPP_BM_584


title: Donor_313C_HSCMPP_BM_585


title: Donor_313C_HSCMPP_BM_583


title: Donor_313C_HSCMPP_BM_581


title: Donor_313C_HSCMPP_BM_582


title: Donor_313C_HSCMPP_BM_577


title: Donor_313C_HSCMPP_BM_600


title: Donor_313C_HSCMPP_BM_580


title: Donor_313C_HSCMPP_BM_579


title: Donor_313C_HSCMPP_BM_574


title: Donor_313C_HSCMPP_BM_575


title: Donor_313C_HSCMPP_BM_578


title: Donor_313C_HSCMPP_BM_568


title: Donor_313C_HSCMPP_BM_576


title: Donor_313C_HSCMPP_BM_571


title: Donor_313C_HSCMPP_BM_565


title: Donor_313C_HSCMPP_BM_569


title: Donor_313C_HSCMPP_BM_566


title: Donor_313C_HSCMPP_BM_572


title: Donor_313C_HSCMPP_BM_567


title: Donor_313C_HSCMPP_PB_562


title: Donor_313C_HSCMPP_PB_563


title: Donor_313C_HSCMPP_BM_564


title: Donor_313C_HSCMPP_BM_558


title: Donor_313C_HSCMPP_PB_561


title: Donor_313C_HSCMPP_BM_559


title: Donor_313C_HSCMPP_BM_555


title: Donor_313C_HSCMPP_BM_557


title: Donor_313C_HSCMPP_BM_552


title: Donor_313C_HSCMPP_BM_554


title: Donor_313C_HSCMPP_PB_551


title: Donor_313C_HSCMPP_BM_553


title: Donor_313C_HSCMPP_BM_573


title: Donor_313C_HSCMPP_PB_550


title: Donor_313C_HSCMPP_PB_549


title: Donor_313C_HSCMPP_BM_547


title: Donor_313C_HSCMPP_PB_548


title: Donor_313C_HSCMPP_BM_570


title: Donor_313C_HSCMPP_BM_545


title: Donor_313C_HSCMPP_PB_560


title: Donor_313C_HSCMPP_BM_543


title: Donor_313C_HSCMPP_BM_544


title: Donor_313C_HSCMPP_PB_537


title: Donor_313C_HSCMPP_BM_541


title: Donor_313C_HSCMPP_BM_542


title: Donor_313C_HSCMPP_BM_556


title: Donor_313C_HSCMPP_PB_538


title: Donor_313C_HSCMPP_PB_539


title: Donor_313C_HSCMPP_BM_531


title: Donor_313C_HSCMPP_BM_532


title: Donor_313C_HSCMPP_BM_535


title: Donor_313C_HSCMPP_BM_534


title: Donor_313C_HSCMPP_PB_536


title: Donor_313C_HSCMPP_BM_533


title: Donor_313C_HSCMPP_BM_529


title: Donor_313C_HSCMPP_BM_528


title: Donor_313C_HSCMPP_BM_546


title: Donor_313C_HSCMPP_PB_524


title: Donor_313C_HSCMPP_BM_523


title: Donor_313C_HSCMPP_BM_522


title: Donor_313C_HSCMPP_BM_521


title: Donor_313C_HSCMPP_BM_520


title: Donor_313C_HSCMPP_BM_519


title: Donor_313C_HSCMPP_BM_540


title: Donor_313C_HSCMPP_BM_517


title: Donor_313C_HSCMPP_BM_516


title: Donor_313C_HSCMPP_BM_530


title: Donor_313C_HSCMPP_SPL_513


title: Donor_313C_HSCMPP_BM_509


title: Donor_313C_HSCMPP_BM_511


title: Donor_313C_HSCMPP_SPL_512


title: Donor_313C_HSCMPP_BM_510


title: Donor_313C_HSCMPP_SPL_514


title: Donor_313C_HSCMPP_BM_508


title: Donor_313C_HSCMPP_PB_527


title: Donor_313C_HSCMPP_SPL_503


title: Donor_313C_HSCMPP_PB_525


title: Donor_313C_HSCMPP_BM_507


title: Donor_313C_HSCMPP_PB_526


title: Donor_313C_HSCMPP_BM_504


title: Donor_313C_HSCMPP_BM_505


title: Donor_313C_HSCMPP_BM_506


title: Donor_313C_HSCMPP_SPL_500


title: Donor_313C_HSCMPP_BM_499


title: Donor_313C_HSCMPP_BM_518


title: Donor_313C_HSCMPP_BM_498


title: Donor_313C_HSCMPP_SPL_502


title: Donor_313C_HSCMPP_BM_496


title: Donor_313C_HSCMPP_BM_497


title: Donor_313C_HSCMPP_BM_494


title: Donor_313C_HSCMPP_SPL_515


title: Donor_313C_HSCMPP_BM_493


title: Donor_313C_HSCMPP_BM_492


title: Donor_313C_HSCMPP_SPL_490


title: Donor_313C_HSCMPP_SPL_488


title: Donor_313C_HSCMPP_BM_487


title: Donor_313C_HSCMPP_BM_486


title: Donor_313C_HSCMPP_SPL_489


title: Donor_313C_HSCMPP_BM_483


title: Donor_313C_HSCMPP_SPL_501


title: Donor_313C_HSCMPP_SPL_478


title: Donor_313C_HSCMPP_SPL_477


title: Donor_313C_HSCMPP_BM_480


title: Donor_313C_HSCMPP_BM_482


title: Donor_313C_HSCMPP_SPL_479


title: Donor_313C_HSCMPP_BM_475


title: Donor_313C_HSCMPP_SPL_476


title: Donor_313C_HSCMPP_BM_495


title: Donor_313C_HSCMPP_BM_473


title: Donor_313C_HSCMPP_BM_471


title: Donor_313C_HSCMPP_BM_474


title: Donor_313C_HSCMPP_BM_472


title: Donor_313C_HSCMPP_BM_469


title: Donor_313C_HSCMPP_BM_468


title: Donor_313C_HSCMPP_BM_467


title: Donor_313C_HSCMPP_BM_470


title: Donor_313C_HSCMPP_SPL_491


title: Donor_313C_HSCMPP_BM_466


title: Donor_313C_HSCMPP_BM_485


title: Donor_313C_HSCMPP_BM_484


title: Donor_313C_HSCMPP_BM_481


title: Donor_313C_HSCMPP_BM_464


title: Donor_313C_HSCMPP_BM_463


title: Donor_313C_HSCMPP_BM_465


title: Donor_313C_HSCMPP_BM_462


title: Donor_313C_HSCMPP_BM_461


title: Donor_313C_HSCMPP_BM_459


title: Donor_313C_HSCMPP_BM_460


title: Donor_313C_HSCMPP_BM_458


title: Donor_313C_HSCMPP_BM_457


title: Donor_313C_HSCMPP_BM_456


title: Donor_313C_HSCMPP_BM_451


title: Donor_313C_HSCMPP_BM_453


title: Donor_313C_HSCMPP_BM_452


title: Donor_313C_HSCMPP_BM_448


title: Donor_313C_HSCMPP_BM_454


title: Donor_313C_HSCMPP_BM_447


title: Donor_313C_HSCMPP_BM_450


title: Donor_313C_HSCMPP_PB_440


title: Donor_313C_HSCMPP_BM_446


title: Donor_313C_HSCMPP_BM_445


title: Donor_313C_HSCMPP_PB_443


title: Donor_313C_HSCMPP_PB_442


title: Donor_313C_HSCMPP_BM_449


title: Donor_313C_HSCMPP_PB_444


title: Donor_313C_HSCMPP_PB_438


title: Donor_313C_HSCMPP_PB_441


title: Donor_313C_HSCMPP_PB_436


title: Donor_313C_HSCMPP_PB_434


title: Donor_313C_HSCMPP_BM_455


title: Donor_313C_HSCMPP_PB_439


title: Donor_313C_HSCMPP_PB_433


title: Donor_313C_HSCMPP_PB_435


title: Donor_313C_HSCMPP_PB_431


title: Donor_313C_HSCMPP_PB_430


title: Donor_313C_HSCMPP_PB_437


title: Donor_313C_HSCMPP_PB_432


title: Donor_313C_HSCMPP_PB_429


title: Donor_313C_HSCMPP_PB_425


title: Donor_313C_HSCMPP_PB_426


title: Donor_313C_HSCMPP_PB_427


title: Donor_313C_HSCMPP_PB_423


title: Donor_313C_HSCMPP_PB_422


title: Donor_313C_HSCMPP_PB_424


title: Donor_313C_HSCMPP_PB_421


title: Donor_313C_HSCMPP_PB_420


title: Donor_313C_HSCMPP_PB_418


title: Donor_313C_HSCMPP_PB_419


title: Donor_313C_HSCMPP_PB_415


title: Donor_313C_HSCMPP_PB_416


title: Donor_313C_HSCMPP_PB_414


title: Donor_313C_HSCMPP_PB_413


title: Donor_313C_HSCMPP_SPL_411


title: Donor_313C_HSCMPP_SPL_412


title: Donor_313C_HSCMPP_SPL_408


title: Donor_313C_HSCMPP_SPL_410


title: Donor_313C_HSCMPP_SPL_407


title: Donor_313C_HSCMPP_PB_417


title: Donor_313C_HSCMPP_SPL_406


title: Donor_313C_HSCMPP_SPL_409


title: Donor_313C_HSCMPP_SPL_405


title: Donor_313C_HSCMPP_PB_428


title: Donor_313C_HSCMPP_SPL_404


title: Donor_313C_HSCMPP_SPL_402


title: Donor_313C_HSCMPP_SPL_400


title: Donor_313C_HSCMPP_SPL_401


title: Donor_313C_HSCMPP_SPL_398


title: Donor_313C_HSCMPP_SPL_403


title: Donor_313C_HSCMPP_SPL_397


title: Donor_313C_HSCMPP_SPL_396


title: Donor_313C_HSCMPP_SPL_394


title: Donor_313C_HSCMPP_SPL_393


title: Donor_313C_HSCMPP_SPL_392


title: Donor_313C_HSCMPP_SPL_395


title: Donor_313C_HSCMPP_SPL_391


title: Donor_313C_HSCMPP_SPL_390


title: Donor_313C_HSCMPP_SPL_386


title: Donor_313C_HSCMPP_SPL_387


title: Donor_313C_HSCMPP_SPL_385


title: Donor_313C_HSCMPP_SPL_388


title: Donor_313C_HSCMPP_SPL_383


title: Donor_313C_HSCMPP_SPL_384


title: Donor_313C_HSCMPP_SPL_381


title: Donor_313C_HSCMPP_SPL_382


title: Donor_207B_HSCMPP_BM_380

value: Donor 1 (207B)

value: 19 years old

value: male

value: Donation after brainstem death (DBD)


title: Donor_207B_HSCMPP_BM_379


title: Donor_313C_HSCMPP_SPL_399


title: Donor_207B_HSCMPP_BM_377


title: Donor_207B_HSCMPP_BM_378


title: Donor_207B_HSCMPP_BM_376


title: Donor_207B_HSCMPP_BM_374


title: Donor_207B_HSCMPP_BM_375


title: Donor_207B_HSCMPP_BM_370


title: Donor_207B_HSCMPP_BM_369


title: Donor_207B_HSCMPP_BM_371


title: Donor_207B_HSCMPP_BM_368


title: Donor_207B_HSCMPP_BM_366


title: Donor_207B_HSCMPP_BM_365


title: Donor_313C_HSCMPP_SPL_389


title: Donor_207B_HSCMPP_BM_367


title: Donor_207B_HSCMPP_BM_362


title: Donor_207B_HSCMPP_BM_363


title: Donor_207B_HSCMPP_BM_364


title: Donor_207B_HSCMPP_BM_361


title: Donor_207B_HSCMPP_BM_358


title: Donor_207B_HSCMPP_BM_360


title: Donor_207B_HSCMPP_BM_356


title: Donor_207B_HSCMPP_BM_359


title: Donor_207B_HSCMPP_BM_352


title: Donor_207B_HSCMPP_BM_355


title: Donor_207B_HSCMPP_BM_353


title: Donor_207B_HSCMPP_BM_354


title: Donor_207B_HSCMPP_BM_373


title: Donor_207B_HSCMPP_BM_351


title: Donor_207B_HSCMPP_BM_372


title: Donor_207B_HSCMPP_BM_350


title: Donor_207B_HSCMPP_BM_348


title: Donor_207B_HSCMPP_BM_349


title: Donor_207B_HSCMPP_BM_345


title: Donor_207B_HSCMPP_BM_346


title: Donor_207B_HSCMPP_BM_347


title: Donor_207B_HSCMPP_BM_344


title: Donor_207B_HSCMPP_BM_343


title: Donor_207B_HSCMPP_BM_342


title: Donor_207B_HSCMPP_BM_341


title: Donor_207B_HSCMPP_BM_340


title: Donor_207B_HSCMPP_BM_339


title: Donor_207B_HSCMPP_BM_337


title: Donor_207B_HSCMPP_BM_357


title: Donor_207B_HSCMPP_BM_336


title: Donor_207B_HSCMPP_BM_338


title: Donor_207B_HSCMPP_BM_333


title: Donor_207B_HSCMPP_BM_331


title: Donor_207B_HSCMPP_BM_330


title: Donor_207B_HSCMPP_BM_327


title: Donor_207B_HSCMPP_BM_328


title: Donor_207B_HSCMPP_BM_326


title: Donor_207B_HSCMPP_BM_334


title: Donor_207B_HSCMPP_BM_325


title: Donor_207B_HSCMPP_BM_332


title: Donor_207B_HSCMPP_BM_324


title: Donor_207B_HSCMPP_BM_319


title: Donor_207B_HSCMPP_BM_320


title: Donor_207B_HSCMPP_BM_317


title: Donor_207B_HSCMPP_BM_323


title: Donor_207B_HSCMPP_BM_322


title: Donor_207B_HSCMPP_BM_321


title: Donor_207B_HSCMPP_BM_329


title: Donor_207B_HSCMPP_BM_318


title: Donor_207B_HSCMPP_BM_316


title: Donor_207B_HSCMPP_BM_314


title: Donor_207B_HSCMPP_BM_312


title: Donor_207B_HSCMPP_BM_335


title: Donor_207B_HSCMPP_BM_311


title: Donor_207B_HSCMPP_BM_313


title: Donor_207B_HSCMPP_BM_310


title: Donor_207B_HSCMPP_BM_309


title: Donor_207B_HSCMPP_BM_306


title: Donor_207B_HSCMPP_BM_307


title: Donor_207B_HSCMPP_BM_308


title: Donor_207B_HSCMPP_BM_304


title: Donor_207B_HSCMPP_BM_305


title: Donor_207B_HSCMPP_BM_301


title: Donor_207B_HSCMPP_BM_302


title: Donor_207B_HSCMPP_BM_300


title: Donor_207B_HSCMPP_BM_295


title: Donor_207B_HSCMPP_BM_296


title: Donor_207B_HSCMPP_BM_299


title: Donor_207B_HSCMPP_BM_297


title: Donor_207B_HSCMPP_BM_292


title: Donor_207B_HSCMPP_BM_293


title: Donor_207B_HSCMPP_BM_289


title: Donor_207B_HSCMPP_BM_290


title: Donor_207B_HSCMPP_BM_315


title: Donor_207B_HSCMPP_BM_294


title: Donor_207B_HSCMPP_BM_291


title: Donor_207B_HSCMPP_BM_298


title: Donor_207B_HSCMPP_BM_288


title: Donor_207B_HSCMPP_SPL_285


title: Donor_207B_HSCMPP_BM_287


title: Donor_207B_HSCMPP_BM_286


title: Donor_207B_HSCMPP_SPL_283


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title: Donor_207B_HSCMPP_SPL_280


title: Donor_207B_HSCMPP_SPL_281


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title: Donor_207B_HSCMPP_SPL_279


title: Donor_207B_HSCMPP_SPL_277


title: Donor_207B_HSCMPP_SPL_276


title: Donor_207B_HSCMPP_SPL_275


title: Donor_207B_HSCMPP_SPL_273


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title: Donor_207B_HSCMPP_SPL_268


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title: Donor_207B_HSCMPP_SPL_257


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title: Donor_207B_HSCMPP_SPL_222


title: Donor_207B_HSCMPP_SPL_221


title: Donor_207B_HSCMPP_SPL_220


title: Donor_207B_HSCMPP_SPL_219


title: Donor_207B_HSCMPP_SPL_218


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title: Donor_207B_HSCMPP_SPL_214


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title: Donor_207B_HSCMPP_SPL_229


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title: Donor_207B_HSCMPP_SPL_234


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title: Donor_207B_HSCMPP_SPL_217


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title: Donor_207B_HSCMPP_SPL_208


title: Donor_207B_HSCMPP_SPL_200


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title: Donor_207B_HSCMPP_SPL_197


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title: Donor_207B_HSCMPP_BM_154


title: Donor_207B_HSCMPP_BM_151


title: Donor_207B_HSCMPP_BM_170


title: Donor_207B_HSCMPP_BM_147


title: Donor_207B_HSCMPP_BM_149


title: Donor_207B_HSCMPP_BM_167


title: Donor_207B_HSCMPP_BM_144


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title: Donor_207B_HSCMPP_BM_145


title: Donor_207B_HSCMPP_BM_164


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title: Donor_207B_HSCMPP_BM_142


title: Donor_207B_HSCMPP_BM_139


title: Donor_207B_HSCMPP_BM_138


title: Donor_207B_HSCMPP_BM_137


title: Donor_207B_HSCMPP_BM_136


title: Donor_207B_HSCMPP_BM_133


title: Donor_207B_HSCMPP_BM_134


title: Donor_207B_HSCMPP_BM_152


title: Donor_207B_HSCMPP_BM_130


title: Donor_207B_HSCMPP_BM_131


title: Donor_207B_HSCMPP_BM_150


title: Donor_207B_HSCMPP_BM_135


title: Donor_207B_HSCMPP_BM_125


title: Donor_207B_HSCMPP_BM_128


title: Donor_207B_HSCMPP_BM_127


title: Donor_207B_HSCMPP_BM_126


title: Donor_207B_HSCMPP_BM_132


title: Donor_207B_HSCMPP_BM_146


title: Donor_207B_HSCMPP_BM_124


title: Donor_207B_HSCMPP_BM_123


title: Donor_207B_HSCMPP_BM_118


title: Donor_207B_HSCMPP_BM_129


title: Donor_207B_HSCMPP_BM_140


title: Donor_207B_HSCMPP_BM_117


title: Donor_207B_HSCMPP_BM_122


title: Donor_207B_HSCMPP_BM_114


title: Donor_207B_HSCMPP_BM_112


title: Donor_207B_HSCMPP_BM_116


title: Donor_207B_HSCMPP_BM_121


title: Donor_207B_HSCMPP_BM_119


title: Donor_207B_HSCMPP_BM_115


title: Donor_207B_HSCMPP_BM_109


title: Donor_207B_HSCMPP_BM_102


title: Donor_207B_HSCMPP_BM_100


title: Donor_207B_HSCMPP_BM_111


title: Donor_207B_HSCMPP_BM_104


title: Donor_207B_HSCMPP_BM_101


title: Donor_207B_HSCMPP_BM_110


title: Donor_207B_HSCMPP_BM_120


title: Donor_207B_HSCMPP_BM_107


title: Donor_207B_HSCMPP_BM_99


title: Donor_207B_HSCMPP_BM_108


title: Donor_207B_HSCMPP_BM_105


title: Donor_207B_HSCMPP_BM_97


title: Donor_207B_HSCMPP_BM_113


title: Donor_207B_HSCMPP_BM_103


title: Donor_207B_HSCMPP_BM_106


title: Donor_207B_HSCMPP_BM_98


title: Donor_207B_HSCMPP_SPL_92


title: Donor_207B_HSCMPP_SPL_93


title: Donor_207B_HSCMPP_SPL_94


title: Donor_207B_HSCMPP_SPL_90


title: Donor_207B_HSCMPP_SPL_91


title: Donor_207B_HSCMPP_SPL_89


title: Donor_207B_HSCMPP_SPL_86


title: Donor_207B_HSCMPP_BM_96


title: Donor_207B_HSCMPP_SPL_87


title: Donor_207B_HSCMPP_SPL_85


title: Donor_207B_HSCMPP_SPL_83


title: Donor_207B_HSCMPP_SPL_84


title: Donor_207B_HSCMPP_SPL_88


title: Donor_207B_HSCMPP_SPL_82


title: Donor_207B_HSCMPP_SPL_95


title: Donor_207B_HSCMPP_SPL_80


title: Donor_207B_HSCMPP_SPL_75


title: Donor_207B_HSCMPP_SPL_78


title: Donor_207B_HSCMPP_SPL_72


title: Donor_207B_HSCMPP_SPL_77


title: Donor_207B_HSCMPP_SPL_79


title: Donor_207B_HSCMPP_SPL_71


title: Donor_207B_HSCMPP_SPL_69


title: Donor_207B_HSCMPP_SPL_81


title: Donor_207B_HSCMPP_SPL_74


title: Donor_207B_HSCMPP_SPL_70


title: Donor_207B_HSCMPP_SPL_67


title: Donor_207B_HSCMPP_SPL_66


title: Donor_207B_HSCMPP_SPL_65


title: Donor_207B_HSCMPP_SPL_73


title: Donor_207B_HSCMPP_SPL_76


title: Donor_207B_HSCMPP_SPL_62


title: Donor_207B_HSCMPP_SPL_60


title: Donor_207B_HSCMPP_SPL_58


title: Donor_207B_HSCMPP_SPL_59


title: Donor_207B_HSCMPP_SPL_61


title: Donor_207B_HSCMPP_SPL_53


title: Donor_207B_HSCMPP_SPL_47


title: Donor_207B_HSCMPP_SPL_63


title: Donor_207B_HSCMPP_SPL_44


title: Donor_207B_HSCMPP_SPL_56


title: Donor_207B_HSCMPP_SPL_43


title: Donor_207B_HSCMPP_SPL_41


title: Donor_207B_HSCMPP_SPL_36


title: Donor_207B_HSCMPP_SPL_54


title: Donor_207B_HSCMPP_SPL_49


title: Donor_207B_HSCMPP_SPL_50


title: Donor_207B_HSCMPP_SPL_46


title: Donor_207B_HSCMPP_SPL_68


title: Donor_207B_HSCMPP_SPL_55


title: Donor_207B_HSCMPP_SPL_64


title: Donor_207B_HSCMPP_SPL_32


title: Donor_207B_HSCMPP_SPL_39


title: Donor_207B_HSCMPP_SPL_48


title: Donor_207B_HSCMPP_SPL_35


title: Donor_207B_HSCMPP_SPL_51


title: Donor_207B_HSCMPP_SPL_45


title: Donor_207B_HSCMPP_SPL_52


title: Donor_207B_HSCMPP_SPL_34


title: Donor_207B_HSCMPP_SPL_40


title: Donor_207B_HSCMPP_SPL_38


title: Donor_207B_HSCMPP_SPL_33


title: Donor_207B_HSCMPP_SPL_27


title: Donor_207B_HSCMPP_SPL_37


title: Donor_207B_HSCMPP_SPL_26


title: Donor_207B_HSCMPP_SPL_57


title: Donor_207B_HSCMPP_SPL_23


title: Donor_207B_HSCMPP_SPL_21


title: Donor_207B_HSCMPP_SPL_28


title: Donor_207B_HSCMPP_SPL_29


title: Donor_207B_HSCMPP_SPL_20


title: Donor_207B_HSCMPP_SPL_42


title: Donor_207B_HSCMPP_SPL_18


title: Donor_207B_HSCMPP_SPL_11


title: Donor_207B_HSCMPP_SPL_12


title: Donor_207B_HSCMPP_SPL_25


title: Donor_207B_HSCMPP_SPL_13


title: Donor_207B_HSCMPP_SPL_15


title: Donor_207B_HSCMPP_SPL_31


title: Donor_207B_HSCMPP_SPL_10


title: Donor_207B_HSCMPP_SPL_8


title: Donor_207B_HSCMPP_SPL_30


title: Donor_207B_HSCMPP_SPL_19


title: Donor_207B_HSCMPP_SPL_7


title: Donor_207B_HSCMPP_SPL_22


title: Donor_207B_HSCMPP_SPL_16


title: Donor_207B_HSCMPP_SPL_4


title: Donor_207B_HSCMPP_SPL_3


title: Donor_207B_HSCMPP_SPL_14


title: Donor_207B_HSCMPP_SPL_24


title: Donor_207B_HSCMPP_SPL_1


title: Donor_207B_HSCMPP_SPL_5


title: Donor_207B_HSCMPP_SPL_6


title: Donor_207B_HSCMPP_SPL_2


title: MSC_Rep3_day5

status: Public on Nov 26 2019

city: Kajang

first: Chee-Yin

last: Wong

state: Selangor

address: Jalan Sungai Long, Bandar Sungai Long

department: Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

data_processing:
The processed reads were then mapped to the GRCh37 reference genome and Ensembl transcriptome version 75 by Tophat (version 2.1.10), as well as its embedded aligner Bowtie 2 (version 2.1.0) using the default parameters.
The mapped reads were assembled by Cufflinks (version 2.2.1) with Ensembl version 75 GTF file and read counts of both gene and transcript levels were summarized by Cuffquant and Cuffnorm within the Cufflinks software suite.
The raw read counts of samples were normalized with the TMM algorithm provided in the R package edgeR  and the batch effects were removed with the ComBat function included in the R sva package.
Genome_build: GRCh37

source_name: MSC differentiated mesangial cells

extract_protocol:
On the indicated days (day 1, 2, 3, 5 and 7), co-cultured MSC were harvested and total RNA was extracted.
Poly-A mRNA selection and synthesis of a cDNA library were carried out according to Illumina TruSeq protocol.

treatment_protocol: MSC were co-cultured with oxidant-injured human mesangial cells in trans-well dishes separated by a membrane for 7 days.

value: MSC differentiated mesangial cells

tag: developmental stage

value: day 5 after co-cultured


title: MSC_Rep2_day7

value: day 7 after co-cultured


title: MSC_Rep3_day3

value: day 3 after co-cultured


title: MSC_Rep3_day7


title: Donor_207B_HSCMPP_SPL_9


title: Donor_207B_HSCMPP_SPL_17


title: MSC_Rep2_day2

value: day 2 after co-cultured


title: MSC_Rep3_day2


title: MSC_Rep2_day5


title: MSC_Rep1_day2


title: MSC_Rep1_day3


title: MSC_Rep1_day7


title: MSC_Rep2_day3


title: MSC_Rep3_day1

value: day 1 after co-cultured


title: MSC_Rep2_day1


title: MapR_U87T_ActD_control_rep2

status: Public on Oct 18 2019

data_processing:
reads were aligned to hg19 using bowtie2
wig files were made from aligned .bam files using DeepTools bamCoverage - normalize using CPM, bin size 10, no read extension
peak calling was done using MACS2 --broadPeak mode from aligned .bam files with default options
peaks in regions of artefactually high signal were removed using ENCODE consensus hg19 blacklist (https://personal.broadinstitute.org/anshul/projects/encode/rawdata/blacklists/)
Genome_build: hg19
Supplementary_files_format_and_content: Normalized .wig files and MACS2 output .broadPeak files filtered by blacklist

growth_protocol: 293  and U87T cells were grown in DMEM-high glucose medium supplemented with 10% calf serum, 3% HEPES, 1% glutamine, 1% non-essential amino acids and 1% penicillin-streptomycin at 37 °C.

extract_protocol:
DNA was collected from the supernatant after treatment with the indicated Mnase-containing fusion proteins as per the CUT&RUN protocol (Skene & Henikoff eLife 2017).
DNA was end-repaired using End-It Repair Kit, tailed with an A using Klenow exo minus, and ligated to custom adapters with T4 DNA ligase. Fragments > 150 bp were size-selected with SPRI and subjected to ligation-mediated PCR amplification (LM-PCR) with custom barcoded adapters for Illumina sequencing using Q5 DNA polymerase. All enzymes except Q5 (NEB) were from Enzymatics (a Qiagen company).

treatment_protocol:
For RNase H treatment, 293 or U87T cells were immobilized on concanavalin beads for 1 hour and then incubated with 150U RNase H in wash buffer containing 20 mM HEPES pH 7.5, 0.15 M NaCl, 0.5 mM Spermidine, 1 mM protease Inhibitor, and 0.02% digitonin. Immobilized cells were processed for MapR detection of R loops.
For Actinomycin D treatment, 293 or U87T cells were treated for 8 hours with 5ug/ml Actinomycin D.  Cells were trypsinized and immobilized on concanavalin beads for 1 hour and processed for MapR detection of R loops.

tag: technology

value: MapR

tag: treatment

value: Actinomycin D

tag: fusion protein

value: GST-MNase


title: MSC_Rep1_day5


title: te-3

status: Public on Oct 29 2019

city: harbin

first: xu

last: yangx

address: mucai 59

country: China

institute: neau

data_processing:
Smart-Seq2 method was used to amplify the single cell sample. The reaction system for the first cDNA strand synthesis comprised the reverse transcription enzyme, buffer, TSO primers and oligo-dT primers with common sequence. For the second strand synthesis, added PCR amplification reagent and ISPCR primer with common sequence to the first strand products. The sample cDNA was fragmented into 300bp by Bioruptor®Sonication System (Diagenode Inc.), and then performed terminal repair, addition of A, and ligation of sequencing adapters, and amplified. The PCR amplification product with 350-450bp was extracted. Then, the concentration was measured by Qubit 2.0 Flurometer (Life Technologies, CA, USA). The integrity of the amplified products was detected by Agilent 2100 High Sensitivity DNA Assay Kit (Agilent Technologies, CA, USA). The libraries were sequenced by an Illumina HiSeq X Ten platform.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

source_name: in vivo embryo

growth_protocol: in vivo embryos

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blastocyst-trophoblast

value: blastomere


title: te-2


title: MSC_Rep1_day1


title: MapR_U87T_RH_rep1

value: RNAse H

value: GST-RH-delta-MNase


title: icm-1

value: blastocyst-inner cell mass


title: MapR_U87T_RH_rep2


title: icm-2


title: MapR_U87T_RH_control_rep2


title: MapR_U87T_control_100K


title: MapR_U87T_control_rep2


title: MapR_U87T_ActD_rep1


title: MapR_U87T_RH_control_rep1


title: MapR_U87T_rep2


title: MapR_U87T_control_rep1_tech1


title: MapR_U87T_rep1_tech1


title: MapR_293_ActD_control_rep2


title: MapR_U87T_100K


title: MapR_U87T_ActD_rep2


title: MapR_293_ActD_rep2


title: MapR_U87T_rep1_tech2

description:
MapR_U87T_rep1.bw
MapR_U87T_rep1.broadPeak.gz


title: MapR_293_ActD_control_rep1


title: MapR_U87T_ActD_control_rep1


title: MapR_293_ActD_rep1


title: MapR_293_RH_control_rep1

value: Rnase H


title: MapR_293_RH_control_rep2


title: MapR_293_RH_rep1


title: RHdcatCnR_293_control_rep2

value: CUT&RUN

tag: transgene

value: RH-delta-mSA-FLAG

tag: antibody

value: IgG


title: RHdcatCnR_293_rep3

value: FLAG


title: RHdcatCnR_293_control_rep1


title: MapR_U87T_control_rep1_tech2


title: MapR_293_control_rep2_tech1


title: MapR_293_control_rep3


title: MapR_293_control_rep2_tech2


title: MapR_293_rep2_tech2

description:
MapR_293_rep2.bw
MapR_293_rep2.broadPeak.gz


title: MapR_293_control_rep1


title: MapR_293_rep2_tech1


title: MapR_293_RH_rep2


title: MapR_293_rep3


title: H3K9me3-D0-rep2

status: Public on Feb 23 2019

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
Formaldehyde crosslinking, H3K9me3 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
H3K9me3_D0.bw

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Hi-C reads were aligned and processed using hiclib
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth per chromosome by downsampling the deeper sequenced experiment
Peak calling was done using EDD version 1.1.7
bigWig files generated using deepTools 2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed files with four columns: chromosome, start position, end position, score;bigwig files

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were prepared from subcutaneous liposuction material. Cells were cultured under proliferative conditions in DMEM/F12 containing 10% fetal calf serum, 10 ng/ml epidermal growth factor (Sigma-Aldrich E9644) and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-7 were used in two independent differentiation experiments, each towards adipose or neuronal lineages.

extract_protocol:
For RNA-seq, total mRNA was isolated from Neu-D1 and Neu-D3 cells using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing. For ChIP-seq of lamin B1, cells at each differentiation time point were fixed with 1% formaldehyde for 10 min, lysed for 10 min in ChIP lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, protease inhibitors and 1 mM PMSF) and sonicated 4 times 10 min in a Bioruptor (Diagenode) to generate 200 base-pair DNA fragments. After sedimentation, the supernatant was collected and diluted 10-fold in RIPA (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors, 1 mM PMSF). Chromatin was incubated overnight at 4oC with the anti-lamin B1 antibody coupled to Dynabeads Protein A/G (Invitrogen). ChIP samples were washed 4 times in ice-cold RIPA, crosslinks reversed and DNA eluted for 6 h at 68oC in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS and 50 ng/µl Proteinase K. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O prior to processing for Illumina library preparation and sequencing. For Hi-C, 25 million cells per time point and differentiation replicate were cross-linked with fresh 1% formaldehyde (Pierce) for 12 min at room temperature on a rocker. Excess formaldehyde was quenched with 0.125 M glycine for 5 min and cells washed 3 times 5 min in ice-cold PBS. Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and protease inhibitors) on ice for 15 min and homogenised by Douncing with a B-pestle (tight) in lysis buffer until nuclei were released, as assessed by microscopy. The lysate was sedimented, the pellet was resuspended in NEBuffer 2 (10 mM Tris-HCl pH 7.9, 50 mM NaCl, 10 mM MgCl2, 1 mM dithiothreitol) containing 0.1% SDS, and incubated at 65oC for 10 min. SDS was quenched on ice with 1% Triton X-100 and the sample digested with HindIII overnight at 37oC. Digested fragments were labelled with biotin-14-dCTP and blunt-end ligated. Crosslinks were reversed at 65oC overnight, the ligated DNA was purified by phenol-chloroform:isoamylalcohol (Ambion), desalted and RNAse-treated. DNA was sheared to ~100-300 base-pairs by Covaris sonication and size-fractionated on AMpure XP magnetic beads (Beckman Coulter). Biotinylated DNA fragments were pulled-down with Streptavidin beads and processed for Illumina adapter ligation and library preparation.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol: Two days before induction of differentiation, proliferating cells (hereafter, ‘Pro’ stage) were harvested and processed for Hi-C or ChIP. For adipogenic differentiation, harvested ‘Pro’ cells were reseeded in DMEM/F12/10% serum without growth factors. Adipogenesis was induced 48 h later (D0) by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Ad-D1 and Ad-D3) and processed for Hi-C or ChIP. Neuronal differentiation was initiated on D0. In brief, medium was removed on D0 and cells were washed twice 4 min in pre-warmed Gibco serum-free DMEM (Thermo Fisher Scientific). Washing medium was removed and differentiation was induced by adding Gibco Neurobasal medium (Thermo Fisher Scientific) supplemented with 1% fetal calf serum, 1x B27 (Thermo Fisher Scientific), 0.5 mM IBMX, 1 µm dexamethasone, 10 µm forskolin, 200 µm 8CTP-cAMP and 10 mM valproic acid. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Neu-D1 and Neu-D3) and processed for Hi-C or RNA isolation for RNA-seq.

value: Day 0

value: ASCs on the day of differentiation induction

tag: chip antibody

value: anti-H3K9me3 antibody (Diagenode pAB-056-050, at 2.5 microgram per 5 million cells)

tag: replicate


title: MapR_293_rep1

value: GST-RH-delta-Mnase


title: H3K9me3-Ad-D3-rep2

description:
Formaldehyde crosslinking, H3K9me3 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
H3K9me3_Ad-D3.bw

tag: time point

value: Day 3

value: ASCs on day 3 after adipogenic induction


title: H3K9me3-D0-rep1


title: H3K9me3-Ad-D3-rep1


title: RHdcatCnR_293_rep2


title: H3K9me3-Ad-D1-rep1

description:
Formaldehyde crosslinking, H3K9me3 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
H3K9me3_Ad-D1.bw

value: Day 1

value: ASCs on day 1 after adipogenic induction


title: H3K9me3-Ad-D1-rep2


title: E16.5_rep1

status: Public on May 17 2019

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

description: scRNA-seq data from isolated male germ cells at E16.5

data_processing:
Raw base call files were demultiplexed using the 10X Genomics Cell Ranger pipeline (v2.1.0) and aligned to the mouse mm10 transcriptome.
A total of 8 transcriptomes (n=3 for E16.5, n=2 for P0, n=2 for P3, and n=1 for P6) were merged in R using the Seurat package 1 (v2.3.2).
Low quality cell transcriptomes and doublets were assessed within each library and excluded using the following criteria: >1,300 genes for E16.5 #1; >1,900 genes and <80,000 UMI counts for E16.5 #2; >1,200 genes for P0 #1; >1,000 genes and <30,000 UMI counts for P0 #2; >1,500 genes and <70,000 UMI counts for P3 #1; <35,000 UMI counts for P3 #2; <40,000 UMI counts for P6. Filtering based on percent mitochondrial genes detected was conservatively set at <25% for all libraries based on visual inspection of overall distribution and the variability of mitochondrial gene content that occurs based on cell type, proliferation status, and developmental state.
Germ cells were isolated from a small number of contaminating cells in the dataset based on Dazl and Ddx4 transcript abundance before the entire dataset was normalized, scaled (“vars.to.regress” included number of genes, number of UMIs, percent mitochondrial transcripts, and age replicate), and dimensionally reduced using Seurat.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Gene-Cell Matrix filled with Raw Read/Expression Values

source_name: testicular germ cells

extract_protocol:
Single cell suspensions of E16.5, P0, P3, or P6 quadruple-transgenic testes were prepared and germ cells isolated using FACS with an SH800 machine (Sony Biotechnology) gating for tdTomato+ cells. Live cells were loaded into a Chromium Controller (10X Genomics, Inc.).
Single-cell cDNA libraries were generated using v2 chemistry according to the manufacturer’s protocol (10X Genomics, Inc.).

value: Mixed C57/B6 and 129

value: male germ cells


title: E16.5_rep2


title: prostate: LNCaP RNA-seq

status: Public on Oct 05 2018

city: Los Angeles

first: Owen

middle: N

last: Witte

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA

data_processing:
TOIL processing pipeline (https://github.com/BD2KGenomics/toil-rnaseq)
RNA-Seq measurements expressed as upper quartile normalized counts, log2 transformed, filtered for coding genes using HUGO
Genome_build: hg38 human genome
Supplementary_files_format_and_content: RSEM and Kallisto outputs

source_name: prostate

extract_protocol: Library preparation performed by Techonology Center for Genomics & Bioinformatics (TCGB) at UCLA. Libraries for mRNA-Seq were prepared with KAPA Stranded RNA-Seq Kit.

value: prostate

value: prostate adenocarcinoma

tag: transplant


title: prostate: 22RV1 RNA-seq


title: prostate: MSKCC-EF1 RNA-seq

value: small cell prostate cancer


title: prostate: PARCB6 RNA-seq

value: transformed prostate basal epithelial

value: NSG mice


title: prostate: NCI-H660 RNA-seq


title: prostate: DU145 RNA-seq


title: RHdcatCnR_293_rep1

value: CUT&RUN

value: RH-delta-mSA-FLAG


title: prostate: PARCB1 RNA-seq