title: BVDV-ind

city: Copenhagen N

first: Troels

middle: K H

last: Scheel

state: Copenhagen

address: Blegdamsvej 3

department: Institute for Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description:
AGO-CLIP
CLIP-seq
CTCC
NFO124N

data_processing:
AGO-CLIP data was processed as described (Moore et al. 2014 Nature Protocols). The deposited CLIP sequences are composed of (i) the index (4 nts), (ii) the RL5 sequence (AGGGAGGACGATGCGG), (iii) a 5N degenerate linker, (iv) the actual read sequence and, depending on read length (iv) a complete or partial RL3 sequence (GTGTCAGTCACTTCCAGCGGATCTCGTATGCCGTCTTCTGCTTG).
Processed reads were aligned to the bovine genome (BosTau7) and BVDV using Bowtie. After mapping, reads were collapsed on coordinates such that only those with sufficiently different degenerate linkers were kept; this distinguished unique binding events from PCR duplicates. miRNA chimeras were mapped to the BVDV genome as previously described in Scheel et al. 2016 Cell Host&Microbe.
Genome_build: BosTau7
Supplementary_files_format_and_content: Table S1. AGO-CLIP alignment statistics. Alignment statistics are given with indication of name of each BVDV mutant (Virus), Time point, Multiplicity of infection (MOI), CLIP- and sequence-experimental ID (CLIP.exp; Seq.pool), sequencing index (Index), the number of unique standard CLIP reads aligned to BosTau7 after collapsing for PCR duplicates (Collapsed.reads.host), the number of unique standard CLIP reads aligned to BVDV after collapsing for PCR duplicates (Collapsed.reads.virus), the total number of collapsed reads (Collapsed.reads), the percentage of reads aligned to the virus of the total number of reads (Virus.reads.perc) and the total number of virus specific chimeras per sample (Total.chimeras.virus). Provided as an Excel file.
Supplementary_files_format_and_content: Table S2. Standard AGO-CLIP reads aligning to the virus presented in BED file format. All individual AGO-CLIP reads mapping to BVDV are listed with chromosome/viral genome (Chr), start coordinate (Start), end coordinate (End), read name (Read_name), Collapse factor (Collapse_factor), strand (Strand) and the experiment name (Sample_name). Provided as an Excel file.
Supplementary_files_format_and_content: Table S3. Virus specific individual miRNA-target chimeras presented in bigBed format. All individual miRNA-target chimeras for each mutant are listed with chromosome/viral genome (Chr), start coordinate (Start), end coordinate (End), miRNA name (miRNA), Collapse factor (Collapse_factor), strand (Strand), and miRNA specific RGB color coding (Color). Provided as an Excel file.

organism: Bos taurus

source_name: MDBK

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lysates were Dnase treated, partially RnaseA digested, clarified by centrifugation, and Argonaute-RNA complexes isolated with pan-Ago 2A8 antibody
Libraries were prepared as in Moore et al. 2014 Nature Protocols, but with the following modifications: A 2nd PCR step was used to introduce library specific indices that were additionally compatible with MiSeq sequencers using version2 chemistry.

value: MDBK

tag: virus infection

value: BVDV-ind

tag: moi

tag: time point (hrs)


title: Second_Col-0_JA_0.5hour_RNAseq_rep2

status: Public on Mar 13 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: RNASeq_Sample 68

library_source: transcriptomic

data_processing:
base-calling using RTA 2.7.7
Sequencing reads were quality trimmed using TrimGalore 0.4.5, then aligned to the TAIR10 genome assembly using TopHat 2.1.1
Reads were counted using HTSeq. Differentially expressed genes were identified using edgeR 3.6.2
Quantification of transcripts was performed using Salmon v0.8.1
The TSIS R package was used to perform the isoform switch analysis
Genome_build: TAIR10 and AtRTD2-QUASI
Supplementary_files_format_and_content: txt file with HTseq read count output

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Three day old etiolated seedlings

growth_protocol: Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.

extract_protocol:
RNeasy Plant Mini Kit (74903, Qiagen)
cDNA library preparation and subsequent single read sequencing was carried as previously described (Song,L et al., 2016) DOI: 10.1126/science.aag1550

treatment_protocol: JA treatment in time series 0-24 h

tag: tissue

value: Three day old etiolated seedlings

tag: genotype

tag: treatment

value: JA treatment for 0.5h


title: BVDV-2xmiR17 (rep2)

description:
AGO-CLIP
CLIP-seq
GGCT
NFO124O

tag: cell line

value: BVDV-2xmiR17 (rep2)


title: CLL_A_del17p_untreated_14

type: genomic

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

country: Germany

institute: University Hospital Ulm

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader with standard recommended settings

data_processing: The raw data were processed using the RnBeads package in R/Bioconductor. Probes known to be cross-reactive (43 230) or overlapping known single-nucleotide polymorphisms (SNPs; 8 704), as well as probes giving unreliable measurements (884 as determined by the Greedycut algorithm) were excluded from analysis. The data from the remaining 432 759 probes were subjected to background subtraction using the Noob method and beta-mixture quantile normalization (BMIQ). This normalization strategy successfully mitigated the inherent bias in β-value distributions between the two different types of probes (Infinium I and II) that are present on the HumanMethylation450 BeadChip. In a subsequent step, probes of non-CpG context (1 251), probes binding to sequences on sex chromosomes (9 917) and probes with low standard deviation (69 867) were filtered out. The data obtained by the remaining 351 724 probes were used in downstream analyses.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: CLL, group A (del(17p) and/or TP53mut, untreated)

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from CD19+ fractions of patients' peripheral blood mononuclear cells (PBMCs) using Qiagen AllPrep Kit according to standard instructions

tag: Sex

value: unknown

value: male

tag: treated

value: no

tag: response to therapy

value: not applicable

value: unmutated

value: yes

value: missense


title: CLL_D_nodel17p_chemosensitive_17

source_name: CLL, group D (no del(17p) or TP53mut, chemosensitive)

value: responded

value: none detected


title: CLL_E_nodel17p_refractory_13

source_name: CLL, group E (no del(17p) or TP53mut, refractory)

value: female

value: refractory


title: Second_Col-0_JA_0.5hour_RNAseq_rep1

description: RNASeq_Sample 67


title: BVDV-2xmiR17 (rep1)

description:
AGO-CLIP
CLIP-seq
CATG
KK00065G

value: BVDV-2xmiR17 (rep1)


title: Tat101C22G_1 (exon)

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

source_name: CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat101C22G vectors (Tat101 contains the first and second exons of HIV-1 Tat protein regulator with the change C22G)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Jurkat-TetOff were maintained in RPMI with 300 ug/ml geneticin and both Jurkat-Tat72 and Jurkat-Tat101 cell lines were maintained in RPMI with 300 ug/ml geneticin 300 ug/ml hygromycin B and (BD Biosciences and Clontech, respectively)

extract_protocol: Extracted with Qiagen RNeasy mini columns (Qiagen)

tag: cell type

value: Jurkat


title: Tat101C22G_3 (exon)


title: CLL_C_del17p_refractory_8

source_name: CLL, group C (del(17p) and/or TP53mut, refractory)

value: mutated

value: in frame deletion; missense


title: CLL_C_del17p_refractory_9

value: in frame insertion


title: Second_Col-0_JA_0hour_RNAseq_rep3

description: RNASeq_Sample 66

value: Three day old etiolated seedlings

value: JA treatment for 0h


title: BVDV-swap

description:
AGO-CLIP
CLIP-seq
GTGC
KK00065E

value: MDBK

value: BVDV-swap


title: Tat101wt_3 (exon)

source_name: CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat101 vectors (Tat101 contains the first and second exons of HIV-1 Tat protein regulator)


title: Tat101wt_2 (exon)


title: BVDV-UUUGUAG/let-7

description:
AGO-CLIP
CLIP-seq
ACCG
KK00065F


title: Second_Col-0_JA_0hour_RNAseq_rep2

description: RNASeq_Sample 65


title: CLL_D_nodel17p_chemosensitive_18

value: male

value: no

value: not applicable


title: Second_Col-0_JA_0hour_RNAseq_rep1

description: RNASeq_Sample 64


title: CLL_B_del17p_relapsed_8

source_name: CLL, group B (del(17p) and/or TP53mut, relapsed)

value: unknown

value: yes

value: relapsed

value: unmutated

value: missense


title: BVDV-2xlet-7

description:
AGO-CLIP
CLIP-seq
TGCA
TS2026J


title: CLL_D_nodel17p_chemosensitive_16

value: female

value: none detected


title: BVDV-let-7p3,4/let-7

description:
AGO-CLIP
CLIP-seq
TCAC
TS2026K


title: Tat101wt_1 (exon)

value: Jurkat


title: First_myc2_JA_4hour_RNAseq_rep2

description: RNASeq_Sample 63

value: myc2 T-DNA mutant

value: JA treatment for 4h


title: Tat72_2 (exon)

source_name: CD4+ T cell line stably transfected with TetOff and pTRE2hyg-Tat72 vectors (Tat72 is the first exon of HIV-1 Tat protein regulator)


title: First_myc2_JA_4hour_RNAseq_rep1

description: RNASeq_Sample 62

value: Three day old etiolated seedlings


title: CLL_A_del17p_untreated_13


title: urothelial carcinoma, P18_S2

city: Lund

first: Nour-al-dain

last: Marzouka

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturers specifications

data_processing:
Control probe filtering and background correction was performed within the BioArray Software Environment (BASE). Only the shared probes in the two platforms were used.
Matrix Non-normalized files: The raw intensity values subjected only to background correction.
Matrix Non-normalized_gene files: To produce matrix for genes, the median for the probes in the same gene was used.  No normalization applied.

source_name: fresh-frozen resection sample of urothelial carcinoma

extract_protocol: Two different extraction methods (RNeasy and AllPrep)

treatment_protocol: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resection at hospitals within the southern healthcare region of Sweden.

tag: tumor stage

value: Ta

tag: tumor grade

tag: days from initial tumor

tag: molecular subtype by gex

value: Uro


title: Tat72_1 (exon)


title: CLL_A_del17p_untreated_12


title: IPECJ87

city: Wageningen

first: Bart

last: van der Hee

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

description: Neonate jejunum cell line

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads checked for quality by FastQC and were trimmed for adaptor sequence using trim_galore, and masked for low-complexity or low-quality sequence (>35 bp), then mapped to SS11.1.91 whole genome using Tophat v2.1.1 (5 bp intron overhang, 0.01 FDR, using Cuffdiff 2.2.1)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: SS11.1.91
Supplementary_files_format_and_content: abundances output Cufflinks and excell file containing all samples and FPKM values

organism: Sus scrofa

growth_protocol: Organoids were grown following procedures by Sato et. al (2011) and van der Hee et. al (2018). IPEC-J2 were grown using standard growth protocols, in DMEM (Gibco) supplemented with 10% v/v FBS and 1% v/v penicillin/streptomycin

extract_protocol:
Organoids were extracted from Matrigel droplets by ice-cold medium and repeated pipetting. IPEC-J2 were extracted using trypsin-EDTA. Tissue was homogenized using a Turrax. All samples were processed following manufacturers protocol from the RNEasy mini kit, with an on-column DNAse I digestion
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were passaged every 5 days for the duration of the experiment

tag: animal

value: Cell line

value: Jejunum

tag: age

value: Passage 87

value: Unknown


title: Tat72_3 (exon)


title: Tat101C22G_2 (exon)


title: BVDV-WT

description:
AGO-CLIP
CLIP-seq
GCAT
KK00065D

value: MDBK

tag: virus infection

value: BVDV-WT


title: TetOff_2 (exon)

source_name: CD4+ T cell line stably transfected with TetOff vector


title: urothelial carcinoma, P11_S2

scan_protocol: According to the manufacturers specifications

value: Tx

value: Gx


title: First_myc2_JA_0hour_RNAseq_rep1

description: RNASeq_Sample 60

value: JA treatment for 0h


title: urothelial carcinoma, P11_S1

label_protocol: According to the manufacturers specifications


title: CLL_D_nodel17p_chemosensitive_15

value: male

value: yes

value: responded

value: unmutated

value: no

value: not applicable


title: TetOff_3 (exon)

value: Jurkat


title: IPECJ91

description: Neonate jejunum cell line

value: Passage 91


title: IPECJ67

description: Neonate jejunum cell line

value: Cell line

value: Passage 67


title: CLL_E_nodel17p_refractory_12

value: unknown

value: refractory

value: none detected


title: TetOff_1 (exon)


title: First_Col-0_JA_4hour_RNAseq_rep2

description: RNASeq_Sample 59

value: Three day old etiolated seedlings

value: JA treatment for 4h


title: CLL_D_nodel17p_chemosensitive_14


title: 14WTJ231

description: Host animal 2

source_name: Jejunum tissue

value: Animal 2

value: Jejunum

value: 5 weeks

value: Topigs 20


title: CLL_E_nodel17p_refractory_11

value: male

value: yes


title: First_Col-0_JA_4hour_RNAseq_rep1

description: RNASeq_Sample 58


title: urothelial carcinoma, P10_S3

value: Uro

tag: same tumor, different assay


title: 13OJ2331

description: Individual replicate 3 animal 2

source_name: Jejunum organoid

value: 12 weeks

value: Organoid


title: urothelial carcinoma, P9_S3

value: Mes (GU by IHC)


title: First_Col-0_JA_0hour_RNAseq_rep2

description: RNASeq_Sample 57

value: JA treatment for 0h


title: 12OJ2321

description: Individual replicate 2 animal 2


title: CLL_D_nodel17p_chemosensitive_13_timepoint1

value: responded

value: unmutated

value: no

value: not applicable


title: urothelial carcinoma, P9_S2


title: 11OJ2311

description: Individual replicate 1 animal 2


title: urothelial carcinoma, P7_S3


title: Dm_S2cell_H4K16_ChIPseq_MOF_RNAi_rep2_IP

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

description: dBRD4=fs(1)h , dBRD4-S indicating short isoform of dBRD4

library_source: genomic

data_processing:
Paired-end 75 bp reads were trimmed (TrimGalore, quality threshhold 20), then mapped using Bowtie2, BAM files of biological replicates were merged using SAM Tools
Coverage files were generated with deepTools3 (v3.0.1) bamCompare with a binsize of 1 (bin size of 10 for H3 profiles). The X chromosome was ignored for scaling. The data was normalized as follows: log2FC over Input for Drosophila H4K16ac, H3, Rpb3; Input subtraction for Drosophila Biotin-dBRD4-S and dBRD4. For Rpb3 profiles SES scaling (signal extraction method) was applied
Genome_build: dm6
Supplementary_files_format_and_content: bigwig file format, Input normalized ChIP enrichments

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells (Invitrogen) were cultured in Express Five SFM media (Thermo Fisher) supplemented with 10% (v/v) Glutamax (Thermo Fisher). Cultures were maintained adherent or in shaking incubators at 27ºC at a speed of 80

extract_protocol:
cells were fixed for 10min in 1.8% of formaldehyde at 23 °C, nuclei were isolated, chromatin was fragmented by sonication (Covaris), The lysate was clarified by centrifugation before immunoprecipitation, and eluted by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using AMPure XP Beads (Beckman Coulter); for Rpb3 ChIP experiments Drosophila Virilis chromatin was added prior to IP as spike control. For Biotin ChIP experiments exogenous Biotin-labeled DNA fragments were added prior to IP as spike control.
NEB Next Ultra II

treatment_protocol: for RNAi: dsRNA was added to the cell culture medium, 10µg dsRNA per 1mio cells, cells were harvested after 4 days of RNAi, for dBRD4 inhibitor treatments: DMSO or inhibitor was added to the cell culture medium

tag: cell line background

value: S2 cells

tag: genotype/variation

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

tag: knockdown or inhibitor treatment

value: MOF RNAi

tag: chip antibody

value: H4K16ac(Merck Milipore, 07-329)


title: 10OJ2333

description: Individual replicate 3 animal 2

value: Animal 2

tag: tissue

value: Jejunum

value: 3 weeks

tag: genotype


title: First_Col-0_JA_0hour_RNAseq_rep1

description: RNASeq_Sample 56

value: Three day old etiolated seedlings

tag: treatment


title: urothelial carcinoma, P5_S2

value: Uro


title: CLL_D_nodel17p_chemosensitive_12

tag: Sex

value: female

value: male

tag: treated

tag: response to therapy

value: none detected


title: Dm_S2cell_H4K16_ChIPseq_NSL1_RNAi_rep2_IP

value: NSL1 RNAi


title: 9OJ2323

description: Individual replicate 2 animal 2

value: Organoid


title: urothelial carcinoma, P5_S1

tag: tumor stage

value: Ta

tag: tumor grade


title: CLL_A_del17p_untreated_10

value: unknown

value: no

value: unmutated

value: yes

value: missense


title: CLL_D_nodel17p_chemosensitive_11

value: not applicable

value: mutated


title: CLL_A_del17p_untreated_11


title: 8OJ2313

description: Individual replicate 1 animal 2

value: Animal 2

value: Jejunum


title: urothelial carcinoma, P2_S2

tag: days from initial tumor

tag: molecular subtype by gex

value: Basal


title: Dm_S2cell_H4K16_ChIPseq_GST_RNAi_rep2_IP

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: control RNAi (GST)

value: H4K16ac(Merck Milipore, 07-329)


title: Dm_S2cell_H4K16_ChIPseq_MOF_RNAi_rep1_IP

value: MOF RNAi


title: Dm_S2cell_H4K16_ChIPseq_NSL1_RNAi_rep1_IP

value: NSL1 RNAi


title: CLL_C_del17p_refractory_7

value: male

value: refractory


title: 6OJ8312

description: Individual replicate 3 animal 1

tag: animal

value: Animal 1

tag: age

value: 12 weeks

value: Organoid


title: 7WTJ81

description: Host animal 1

value: 5 weeks

value: Topigs 20


title: CLL_E_nodel17p_refractory_9

value: yes

value: mutated

value: no

value: none detected

value: not applicable


title: Dm_S2cell_H4K16_ChIPseq_GST_RNAi_rep1_IP

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin


title: ACD_5_N

city: Atlanta, Georgia, USA

first: Liang

last: Han

state: GA

address: 950 Atlantic Dr.

department: Biological Sciences

institute: Georgia Institute of Technology

data_processing:
RNA-seq was performed with the illumina HiSeqTM 4000 at a depth of 50 million single-end reads of 50 bp.
Clean reads are mapped to reference genome by Bowtie2 (Langmead and Salzberg, 2012), and then mapped read counts were normalized to the number of Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: spreadsheet include FPKM values for all samples

organism: Mus musculus

extract_protocol:
MrgprA3+ and MrgprA3- neurons from every animal were collected and subjected to FACS. MrgprA3+ neurons were collected based on GFP fluorescent. FACS gating for MrgprA3- cells was selected to collect cells that have similar morphological characteristics as the GFP+ cells in an effort to minimize contamination from other cell types such as satellite glial cells, Schwann cells, and endothelial cells whose sizes are much smaller than sensory neurons. RNA was isolated using the RNeasy Micro Kits (Qiagen).
Polyadenylated mRNA libraries were generated for cDNA library construction, amplification, and sequencing

treatment_protocol: A mouse model of allergic contact dermatitis was produced as described previously with 2-month old males (25 - 30g) C57BL/6 mice (Zhu et al., 2017). Briefly, on day 1-3, SADBE (squaric acid dibutylester, 25ul, 0.5% in acetone) was applied to the shaved abdomen once a day. On days 8-12, SADBE was applied to the shaved lower back skin to induce dermal inflammation. 5 mice were used in both the SADBE treatment group and the control group. On day 13, animals were first recorded for 60 min to examine scratching behaviors and then thoracic and lumbar DRGs (T11-L6, totally 16 DRGs) innervating the treated skin area from every animal were isolated for FACS. We use T12 DRG as the landmark to identify the axial level of all collected DRGs. T12 DRG is the ganglion immediately caudal to the last rib of the animal. Treated skin was also collected for histological analysis at the same time. Mice in the control group were handled exactly the same way as the mice in SADBE group by the experimenters, but were only treated with acetone which is the solvent for SADBE.

tag: strain background

value: 2-month old

value: MrgprA3- (N)

value: allergic contact dermatitis (ACD) condition

value: DRG neurons


title: ACD_4_N


title: Dm_S2cell_H3_ChIPseq_MOF_RNAi_rep2_IP

tag: cell line background

value: MOF RNAi

value: H3 (Abcam, Ab1791)


title: ACD_3_N

tag: genotype/variation


title: 4OJ8112

description: Individual replicate 1 animal 1

value: Animal 1

value: Jejunum

value: 12 weeks


title: ACD_2_N


title: Dm_S2cell_H3_ChIPseq_GST_RNAi_rep2_IP

tag: knockdown or inhibitor treatment

value: control RNAi (GST)


title: ACD_1_N


title: CLL_C_del17p_refractory_6

value: unknown

value: female

value: yes

value: refractory

value: unmutated

value: frameshift; frameshift


title: 5OJ8212

description: Individual replicate 2 animal 1

value: Organoid


title: CLL_B_del17p_relapsed_7

value: male

value: relapsed

value: no

value: in frame deletion


title: CLL_B_del17p_relapsed_6

value: missense


title: ACD_5_GFP

source_name: ACD_GFP_DRG neurons

value: 2-month old

value: genetically labeled MrgprA3+ (GFP)

value: allergic contact dermatitis (ACD) condition

value: DRG neurons


title: CLL_D_nodel17p_chemosensitive_10

value: not applicable

value: mutated

value: none detected


title: RNA-seq_WT hMSCs_2

city: Beijing

first: ji

middle: qian

last: zhao

address: 15 Datun Road Chaoyang District

country: China

institute: institute of zoology ,CAS

description:
RNA sequencing of WT hMSCs.
P10_WT_2.txt

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file of RPKM normalized read cout for each 10 bp bin size for others sequencing data.wig file of  read cout for each 500000 bp bin size for others sequencing data.

source_name: Mesenchymal stem cell

extract_protocol: For CNV analysis, the sequencing libraries were constructed via the Next DNA Library Prep Reagent Set for Illumina (NEB). For ATAC-seq, library was amplified and purified using TruePrep DNA Library Prep Kit V2 for Illumina(Vazyme Biotech). For DamID-seq, the DNA library was established via aNEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. For ChIP-seq, the enriched fragments were constructed into libraries without the incorporation of spike-in controls via KAPA Hyper Prep Kits with PCR Library Ampliﬁcation/Illumina series (KK8504) following the manufacturer’s instructions. For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell type

value: Mesenchymal stem cell

value: WT hMSCs

tag: passage


title: Dm_S2cell_H3_ChIPseq_NSL1_RNAi_rep1_IP

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: NSL1 RNAi

tag: chip antibody

value: H3 (Abcam, Ab1791)


title: 1OJ813

description: Individual replicate 1 animal 1

value: Animal 1

tag: tissue

value: Jejunum

value: 3 weeks

tag: genotype

value: Organoid


title: CLL_A_del17p_untreated_8

tag: Sex

value: unknown

value: male

tag: treated

value: no

value: unmutated

value: yes

value: missense


title: Dm_S2cell_H3_ChIPseq_GST_RNAi_rep1_IP

value: control RNAi (GST)


title: 3OJ833

description: Individual replicate 3 animal 1


title: CLL_A_del17p_untreated_9

tag: response to therapy

value: not applicable


title: Dm_S2cell_H3_ChIPseq_MOF_RNAi_rep1_IP

value: MOF RNAi


title: RNA-seq_ZKSCAN3 defecient hMSCs_2

description:
RNA sequencing of ZKSCAN3 deficient hMSCs.
P10_ZKSCAN3_KO_2.txt

value: Mesenchymal stem cell

value: ZKSCAN3 defecient hMSCs


title: ACD_1_GFP

value: 2-month old

value: genetically labeled MrgprA3+ (GFP)

tag: treatment

value: allergic contact dermatitis (ACD) condition

value: DRG neurons


title: Dm_S2cell_ChIPseq_NSL1_RNAi_rep2_Input

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: NSL1 RNAi


title: Dm_S2cell_ChIPseq_MOF_RNAi_rep2_Input


title: CLL_E_nodel17p_refractory_8

value: male

value: refractory

value: none detected


title: RNA-seq_ZKSCAN3 defecient hMSCs_1

description:
RNA sequencing of ZKSCAN3 deficient hMSCs.
P10_ZKSCAN3_KO_1.txt


title: CLL_D_nodel17p_chemosensitive_9

value: no

value: unmutated

value: yes


title: Dm_S2cell_H3_ChIPseq_NSL1_RNAi_rep2_IP

value: H3 (Abcam, Ab1791)


title: CLL_E_nodel17p_refractory_10

value: female

value: not applicable


title: First_myc2_JA_0hour_RNAseq_rep2

description: RNASeq_Sample 61

value: Three day old etiolated seedlings

value: myc2 T-DNA mutant

value: JA treatment for 0h


title: Dm_S2cell_ChIPseq_GST_RNAi_rep2_Input

value: control RNAi (GST)


title: CNV sequencing_WT hESCs

description:
CNV sequencing of WT hESCs.
ESC_H9_P10_read.wig

data_processing:
Library strategy: DNA-seq
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file of RPKM normalized read cout for each 10 bp bin size for others sequencing data.wig file of  read cout for each 500000 bp bin size for others sequencing data.

source_name: Embryonic stem cell

value: Embryonic stem cell

value: WT hESCs


title: Ctrl_4_N

value: 2-month old

value: MrgprA3- (N)

value: Control condition

value: DRG neurons


title: 2OJ823

description: Individual replicate 2 animal 1

value: Animal 1

value: Jejunum

value: 3 weeks

value: Organoid


title: CNV sequencing_ZKSCAN3 defecient hESCs

description:
CNV sequencing of ZKSCAN3 deficient hESCs.
ESC_ZK3_P10_read.wig

value: ZKSCAN3 defecient hESCs


title: Ctrl_3_N


title: Ctrl_5_N


title: Dm_S2cell_ChIPseq_MOF_RNAi_rep1_Input

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: MOF RNAi


title: CLL_E_nodel17p_refractory_7

value: male

value: yes

value: refractory

value: unmutated

value: no

value: none detected

value: not applicable


title: CLL_D_nodel17p_chemosensitive_8


title: Dm_S2cell_ChIPseq_NSL1_RNAi_rep1_Input

value: NSL1 RNAi


title: ACD_2_GFP

value: 2-month old

value: genetically labeled MrgprA3+ (GFP)

value: allergic contact dermatitis (ACD) condition

value: DRG neurons


title: CNV sequencing_WT hMSCs

description:
CNV sequencing of WT hMSCs.
MSC_H9_P10_read.wig

value: Mesenchymal stem cell

value: WT hMSCs


title: Ctrl_2_N

value: MrgprA3- (N)

value: Control condition


title: Dm_S2cell_ChIPseq_GST_RNAi_rep1_Input

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: control RNAi (GST)


title: Ctrl_1_N


title: CNV sequencing_ZKSCAN3 defecient hMSCs

description:
CNV sequencing of ZKSCAN3 deficient hMSCs.
MSC_ZK3_P10_read.wig

value: ZKSCAN3 defecient hMSCs


title: Dm_S2cell_dBRD4_ChIPseq_GST_RNAi_rep2_IP

value: wild type

value: dBRD4 antibody reconizing short and long isoform ID166 (Paro lab)


title: Ctrl_5_GFP

source_name: Ctrl_GFP_DRG neurons


title: Dm_S2cell_dBRD4_ChIPseq_GST_RNAi_rep1_IP

value: dBRD4antibody reconizing short and long isoform ID166 (Paro lab)


title: Ctrl_4_GFP


title: CLL_E_nodel17p_refractory_6

value: unknown

value: male

value: yes

value: refractory

value: unmutated

value: no

value: none detected

value: not applicable


title: CLL_B_del17p_relapsed_5

value: relapsed

value: in frame deletion


title: input_WT hMSCs

description:
Input file corresponding to H3K9me3 ChIP-seq data of WT hMSCs.
WT_bin10_nohg19.bw

value: Mesenchymal stem cell

value: WT hMSCs

value: none (input)


title: input_ZKSCAN3 defecient hMSCs

description:
Input file corresponding to H3K9me3 ChIP-seq data of ZKSCAN3 deficient hMSCs.
ZK3_bin10_nohg19.bw

value: ZKSCAN3 defecient hMSCs


title: CLL_C_del17p_refractory_4

value: missense


title: Ctrl_3_GFP

value: 2-month old

value: genetically labeled MrgprA3+ (GFP)

value: Control condition

value: DRG neurons


title: Dm_S2cell_dBRD4_ChIPseq_GST_RNAi_rep1_Input

value: S2 cells

value: wild type

value: control RNAi (GST)

value: dBRD4 antibody reconizing short and long isoform ID166 (Paro lab)


title: Ctrl_2_GFP


title: CLL_C_del17p_refractory_5

value: unknown

value: male

value: yes

value: refractory

value: unmutated

value: no

value: frameshift; in frame deletion


title: CLL_B_del17p_relapsed_4

value: relapsed


title: ChIP-seq_WT hMSCs_2

description:
H3K9me3 ChIP-seq of WT hMSCs.
WT_bin10_nohg19.bw

value: Mesenchymal stem cell

value: WT hMSCs

value: H3K9me3 Abcam ab8898


title: CLL_A_del17p_untreated_7

value: female

value: not applicable

value: none detected


title: Ctrl_1_GFP

value: 2-month old

value: genetically labeled MrgprA3+ (GFP)

value: Control condition

value: DRG neurons


title: ACD_4_GFP

value: allergic contact dermatitis (ACD) condition


title: CLL_E_nodel17p_refractory_5

value: unknown

value: yes

value: mutated


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_MOF_RNAi_rep2_IP

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: MOF RNAi

value: streptavidin T1 magnetic beads (Invitrogen 65601)


title: ChIP-seq_WT hMSCs_1

value: Mesenchymal stem cell

value: WT hMSCs


title: Dm_S2cell_dBRD4_ChIPseq_GST_RNAi_rep2_Input

value: wild type

value: control RNAi (GST)

value: dBRD4 antibody reconizing short and long isoform ID166 (Paro lab)


title: ChIP-seq_ZKSCAN3 defecient hMSCs_2

description:
H3K9me3 ChIP-seq of ZKSCAN3 deficient hMSCs.
ZK3_bin10_nohg19.bw

value: ZKSCAN3 defecient hMSCs

value: H3K9me3 Abcam ab8898


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_NSL1_RNAi_rep2_IP

value: NSL1 RNAi


title: ChIP-seq_ZKSCAN3 defecient hMSCs_1


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_GST_RNAi_rep2_IP


title: CLL_A_del17p_untreated_6

value: female

value: no

value: not applicable

value: missense


title: CLL_D_nodel17p_chemosensitive_7

value: unmutated

value: none detected


title: 6419 c5 +Tgfb [SY28]

city: Philadelphia

first: Salina

last: Yuan

state: PA

address: 421 Curie Blvd

department: Medicine

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to the mouse (GRCm38, May 23 2014) reference using STAR (v2.5.1) with default settings.
Raw counts of gene transcripts were obtained using featureCounts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.mm10.featureCounts.gene.txt: Tab-delimited text files include raw counts.

source_name: pancreatic cancer cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum, 10% glutamine, and 150 µg/mL gentamicin at 37°C, 5% CO2, 21% O2, and 100% humidity.

extract_protocol:
RNA was prepared from cultured tumor cells or sorted cells using the RNeasy Mini Kit (Qiagen) according to manufacturer's protocol.
Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries. Libraries were constructed by Novogene (Beijing, China).

treatment_protocol: Cells were treated with 10ng/mL Tgf-b for 4 days.

value: wildtype

value: Pancreatic cancer cells

value: 7 days Tgfb treatment


title: 6419 c5 +Tgfb [SY27]

value: 6 days Tgfb treatment


title: Dam-Emerin_WT hMSCs_3

description:
DamID sequencing of WT hMSCs.
WT_P10_EMDvsDam_bin10.bw

data_processing:
Library strategy: DamID-seq
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file of RPKM normalized read cout for each 10 bp bin size for others sequencing data.wig file of  read cout for each 500000 bp bin size for others sequencing data.

value: Mesenchymal stem cell

value: WT hMSCs

tag: dam-tagged protein

value: Dam-Emerin


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_WT_untagged_control_rep2_IP

value: S2 cells

value: wild type

value: WT

value: streptavidin T1 magnetic beads (Invitrogen 65601)


title: RNA-seq_WT hMSCs_1

description:
RNA sequencing of WT hMSCs.
P10_WT_1.txt


title: Dam-Emerin_WT hMSCs_2


title: 6694 c2 +Tgfb [SY26]

value: 5 days Tgfb treatment


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_MOF_RNAi_rep1_IP

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: MOF RNAi


title: 6694 c2 +Tgfb [SY25]

value: 4 days Tgfb treatment


title: CLL_C_del17p_refractory_3

value: unknown

value: male

value: yes

value: refractory

value: mutated

value: no

value: splice site; missense


title: Dam-Emerin_ZKSCAN3 defecient hMSCs_3

description:
DamID sequencing of ZKSCAN3 deficient hMSCs.
ZK3_P10_EMDvsDam_bin10.bw

value: Mesenchymal stem cell

value: ZKSCAN3 defecient hMSCs


title: 3077 c4 Nsd2 KO c4 [SY24]

value: Pancreatic cancer cells


title: 3077 c4 Nsd2 KO c1 [SY23]


title: CLL_E_nodel17p_refractory_4

value: unmutated

value: none detected

value: not applicable


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_GST_RNAi_rep1_IP

value: S2 cells

value: control RNAi (GST)

value: streptavidin T1 magnetic beads (Invitrogen 65601)


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_WT_untagged_control_rep1_IP

value: wild type

value: WT


title: 3077 c4 WT [SY22]

value: wildtype


title: Dam-Emerin_WT hMSCs_1

value: WT hMSCs

value: Dam-Emerin


title: CLL_D_nodel17p_chemosensitive_6

value: male

value: yes

value: responded


title: 3077 c4 Nsd2 KO c4 [SY21]


title: CLL_A_del17p_untreated_5

source_name: CLL, group A (del(17p) and/or TP53mut, untreated)

value: female

value: no

value: mutated


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_NSL1_RNAi_rep1_IP

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: NSL1 RNAi


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_MOF_RNAi_rep2_Input

value: MOF RNAi


title: DamOnly_WT hMSCs_3

value: Mesenchymal stem cell

value: none (Dam only control)


title: 3077 c4 Nsd2 KO c1 [SY20]

value: Pancreatic cancer cells


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_GST_RNAi_rep2_Input

value: S2 cells

value: control RNAi (GST)

value: streptavidin T1 magnetic beads (Invitrogen 65601)


title: CLL_A_del17p_untreated_4

value: not applicable

value: unmutated

value: none detected


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_NSL1_RNAi_rep2_Input


title: DamOnly_WT hMSCs_1

value: WT hMSCs


title: CLL_D_nodel17p_chemosensitive_5

source_name: CLL, group D (no del(17p) or TP53mut, chemosensitive)

value: yes


title: CLL_B_del17p_relapsed_3

value: unknown

value: male

value: relapsed

value: missense


title: DamOnly_ZKSCAN3 defecient hMSCs_3

value: ZKSCAN3 defecient hMSCs


title: 6419 c5 Kdm2a c1 [SY17]


title: DamOnly_WT hMSCs_2


title: 3077 c4 WT [SY19]

value: wildtype


title: Dm_S2cell_Biotin-dBRD4-S_ChIPseq_WT_untagged_control_rep2_Input

value: wild type

value: WT


title: CLL_D_nodel17p_chemosensitive_4

value: no

value: mutated


title: 6419 c5 Kdm2a c21 [SY18]

value: Pancreatic cancer cells


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_MOF_RNAi_rep1_Input

value: S2 cells

value: S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin

value: MOF RNAi

value: streptavidin T1 magnetic beads (Invitrogen 65601)


title: DamOnly_ZKSCAN3 defecient hMSCs_2

value: Mesenchymal stem cell

value: none (Dam only control)


title: Dam-Emerin_ZKSCAN3 defecient hMSCs_2

value: Dam-Emerin


title: CLL_D_nodel17p_chemosensitive_3

value: male

value: not applicable

value: unmutated

value: none detected


title: 6419 c5 WT [SY16]

value: wildtype


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_NSL1_RNAi_rep1_Input

value: NSL1 RNAi


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_GST_RNAi_rep1_Input

value: control RNAi (GST)


title: DamOnly_ZKSCAN3 defecient hMSCs_1

value: ZKSCAN3 defecient hMSCs


title: ATAC-seq_WT hMSCs_3

description:
ATAC sequencing of WT hMSCs.
WT_bin10_extend_250.bw

value: WT hMSCs


title: Dm_S2cell_Biotin_dBRD4-S_ChIPseq_WT_untagged_control_rep1_Input

value: wild type

value: WT


title: Panc02 Nsd1 KO c1 [SY14]

value: Pancreatic cancer cells


title: H3K9me3_ChIPSeq_DIcer2 kd rescue CHARRs

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
Clean reads were mapped to the reference Drosophila genome (dm6) using Bowtie2.
Enriched peaks were detected by MACS2 with input data as control using the parameters -f BAMPE --nomodel --keep-dup all --broad.
The wig files of each chromatin mark ChIP-seq dataset was obtained by using bamCoverage tools from Deeptools with the parameters: --binSize 1000, --normalizeTo1x 142573017 and --ignoreForNormalization chrM.
Genome_build: dm6

source_name: S2 cells

extract_protocol: For ChIP sequencing, DNA libraries were constructed using the NEBNext® UltraTM II DNA Library Prep kit (NEB, USA) following manufacturer’s recommendations. After end Repair, 5 ́ phosphorylation and dA-Tailing of purified DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated and he library fragments were purified with SPRIselect sample purification beads (NEB, USA). At last, PCR products were purified, and library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced at the Annoroad Gene Technology (Beijing, China) on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

tag: antibody

value: DIcer2 kd rescue CHARRs

tag: cell line

value: S2 cells

tag: passages


title: ATAC-seq_WT hMSCs_2

value: Mesenchymal stem cell


title: Panc02 WT [SY13]


title: Panc02 Nsd1 KO c4 [SY15]


title: ATAC-seq_WT hMSCs_1


title: VLP DNA long read ddm1rdr6

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

description: Instrument model: ONT GridION X5

data_processing:
Library strategy: DNA-seq
RNA-seq: FASTQ files were processed for adaptor trimming using cutadapt. Tophat v2.0.12 was used for mapping. Cuffnorm was used to obtain FPKM values from bam files.
Small RNA-seq: After trimming the 3’ adapter and filtering collapsed reads according to length and quality, filtered reads were mapped with bowtie reporting all multi-mappers. Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Short read VLP DNA-seq: Adapters were trimmed from raw reads with Skewer in paired-end mode and read pairs with both mates longer than 25 nt were retained.
Short read VLP DNA-seq: Reads were aligned to the TAIR10 genome with STAR in two-pass mode to improve spliced alignment at unannotated introns. Reads mapping equally well to multiple locations were randomly assigned, and chimeric/split read alignments were output separately from concordant alignments. Optical and PCR duplicates were removed from the alignments with picard-tools (http://broadinstitute.github.io/picard). Genome-wide coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped. Pairwise differential expression at TAIR10 transposon loci was tested across three wild-type, two ddm1, and three ddm1rdr6 replicates using quasi-likelihood F-tests in edgeR, controlling FDR at 5% and a log2(fold-change) threshold of 2.
Long read VLP DNA-seq: Basecalling was performed offline with Guppy v2.3.1 using the default model. Using porechop (https://github.com/rrwick/Porechop), ONT sequencing adapters were trimmed from 5’ ends, 3’ ends, and the middle of raw reads. Reads with middle adapters were split.
Long read VLP DNA-seq: Remaining reads longer than 100 bp were aligned to the TAIR10 reference with minimap2 for coverage and read alignment plots. Structural variants were called on NGMLR alignments using Sniffles with default parameters, except minimum read support was reduced to 3. RPM-normalized coverage was calculated with bamCoverage from deepTools and normalized to reads per million mapped.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values are shown for each gene identification (ID)
Supplementary_files_format_and_content: Small RNA-seq: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
Supplementary_files_format_and_content: Short read VLP DNA-seq: bigWig
Supplementary_files_format_and_content: Long read VLP DNA-seq: bigWig, vcf (Structural variant calls produced by Sniffles on nanopore long-read alignments to the TAIR10 genome. The number of reads supporting each SV call is given in the RE tag.)

molecule: other

source_name: 4 week-old whole inflorescence stems

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were grown on ½ Murashige and Skoog (MS) medium and seedlings were transplanted to soil 7 day after germination.

extract_protocol:
VLPs were isolated using sucrose buffer and ultracentrifugation. DNase I was treated to remove genomic DNA. After RNase A and proteinase K treatments, VLP DNA was extracted with phenol:chloroform.
Oxford Nanopore (ONT) Long-read libraries were prepared as follows: 10 ng per genotype of purified VLP DNA extract was initially amplified following the conditions in the “1D Low-input genomic DNA with PCR” protocol with SQK-LSK108 reagents. End-repair, dA-tailing and PCR adapter ligation were performed, followed by 16 cycles of PCR amplification. PCR products were purified and concentrated with Ampure XP beads (Agencourt), and 300 ng of eluate per sample was carried through to library preparation following the “1D Genomic DNA by Ligation” protocol with SKQ-LSK109 reagents. Libraries were sequenced on r9.4 flowcells.

tag: ecotype

value: 4 week-old whole inflorescence stems

tag: fraction

value: VLP DNA


title: CLL_E_nodel17p_refractory_3

source_name: CLL, group E (no del(17p) or TP53mut, refractory)

value: unknown

value: female

value: yes

value: refractory

value: no


title: CLL_D_nodel17p_chemosensitive_2

value: not applicable

value: unmutated

value: none detected


title: CLL_A_del17p_untreated_3

value: male


title: H3K9me3_ChIPSeq_DIcer2 kd rescue Scramble

tag: genotype/variation

value: DIcer2 kd rescue Scramble


title: H3K9me3_ChIPSeq_Dicer2 kd

value: Dicer2 kd


title: CLL_E_nodel17p_refractory_1


title: CLL_D_nodel17p_chemosensitive_1

value: responded


title: 6694 c2 Kdm2a KO c6 [SY12]

value: Pancreatic cancer cells


title: 6694 c2 Kdm2a KO c5 [SY11]


title: CLL_E_nodel17p_refractory_2

value: mutated


title: CLL_C_del17p_refractory_2

source_name: CLL, group C (del(17p) and/or TP53mut, refractory)

value: missense


title: VLP DNA long read wild-type

description: Instrument model: ONT GridION X5

value: wild-type

value: 4 week-old whole inflorescence stems


title: ATAC-seq_ZKSCAN3 defecient hMSCs_2

description:
ATAC sequencing of ZKSCAN3 deficient hMSCs.
ZK3_bin10_extend_250.bw

value: Mesenchymal stem cell

value: ZKSCAN3 defecient hMSCs


title: H3K9me3_ChIPSeq_NC

value: NC

value: S2 cells


title: VLP DNA long read ddm1

description: Instrument model: ONT GridION X5

value: VLP DNA


title: CLL_C_del17p_refractory_1

value: female

value: yes

value: refractory

value: no


title: 6419 c5 Kdm2a c21 [SY9]


title: H3K27me3_ChIPSeq_DIcer2 kd rescue Scramble

value: DIcer2 kd rescue Scramble


title: H3K27me3_ChIPSeq_DIcer2 kd rescue CHARRs

value: DIcer2 kd rescue CHARRs


title: TIBbeforeNAC: Human tumor-infiltrating B cells before neoadjuvant chemotherapy

city: Guangzhou

first: Jian-You

last: Liao

state: Guangdong

address: 107# Yanjiang West Road

department: Sun Yat-Sen Memorial Hospital

institute: Sun Yat-Sen University

description: single-cell mRNA

data_processing:
ScRNA-Seq data was processed using 10× Genomics CellRanger V2.1.1 pipeline. The resulting fastq files were passed to CellRanger’s count, which aligned all reads against GRCh38 genomes using the STAR aligner. The data from libraries were pooled by running through CellRanger aggr to obtain unique molecular identifiers (UMIs) matrices. The UMI count matrix were processed using the R package Seurat (version 2.2.1). Both mkfastq and count were run with default parameters.
For each sample, the gene - barcode matrix was passed to the R (v. 3.5.3) software package Seurat (https://satijalab.org/seurat) (v2.2.1) for all downstream analyses. To remove doublets and poor-quality cells, cells were excluded from subsequent analysis if they were outliers in terms of number of genes, number of UMIs, and percentage of mitochondrial genes using Seurat. Consequently, 2,497 single cells (998 from pre-treatment samples and 1,499 from post-treatment samples) were used for the following analyses. The cells were clustered using Seurat's FindClusters. T-distributed stochastic neighbor embedding (t-SNE) and modularity heatmap were created for graph-based cluster identification and subsequent dimensionality reduction. Marker genes for the individual clusters were identified using Seurat’s FindAllMarkers and only significantly upregulated markers (minimum log.FC ≥0 and FDR ≤ 1 × 10-75) were represented.
Genome_build: hg38
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: B cells

extract_protocol:
Cells were isolated from breast tumor tissues of breast cancer patients by flow cytometry.
ScRNA-seq libraries were constructed using Chromium Single Cell 3’ Reagent Kits v3 (10× GENOMICS) according to the manufacturer’s protocol.

treatment_protocol: Sample 2 derived from patients who received four cycles of neoadjuvant chemotherapy.

value: B cells

value: breast tumor tissues


title: TIBafterNAC: Human tumor-infiltrating B cells after neoadjuvant chemotherapy

description: single-cell mRNA


title: ATAC-seq_ZKSCAN3 defecient hMSCs_1


title: 6694 c2 WT [SY10]

value: wildtype

value: Pancreatic cancer cells


title: CLL_B_del17p_relapsed_2

source_name: CLL, group B (del(17p) and/or TP53mut, relapsed)

value: unknown

value: male

value: relapsed

value: unmutated

value: missense; missense


title: H3K27me3_ChIPSeq_Dicer2 kd

value: Dicer2 kd

value: S2 cells


title: CLL_A_del17p_untreated_1

value: female

value: not applicable

value: missense


title: Panc02 Nsd1 KO c4 [SY6]


title: H3K4me3_ChIPSeq_DIcer2 kd rescue CHARRs


title: 6419 c5 Kdm2a c1 [SY8]


title: Panc02 Nsd1 KO c1 [SY5]


title: CLL_B_del17p_relapsed_1

value: yes

value: no

value: missense; in frame deletion


title: 6419 c5 WT [SY7]


title: H3K4me3_ChIPSeq_DIcer2 kd rescue Scramble

value: DIcer2 kd rescue Scramble


title: Panc02 WT [SY4]


title: H3K4me3_ChIPSeq_Dicer2 kd


title: 6694 c2 Kdm2a KO c6 [SY3]


title: H3K27me3_ChIPSeq_NC

value: NC


title: H3K4me3_ChIPSeq_NC


title: SAMPLE 16: Mixture of RNA samples from RifS donor and RifS recipient replicate 1

city: Tsukuba

first: Masatoshi

last: Miyakoshi

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifS donor and RifS recipient, respectively.  It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2440, RNA extracted separately

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Each donor or recipient strain grown overnight was inoculated into a fresh 5 mL LB medium by 100-fold dilution. The cells grown to stationary phase (OD600 of 2.0) were harvested by centrifugation, and resuspended into 500 µL LB medium containing Rif. After mixing the donor and recipient cells in combinations of RifR and RifS isogenic strains, 100 µL of each mixture was immediately spotted on a membrane filter (Advantec), which was placed onto LB agar plate containing Rif to allow the cells to conjugate at 30ºC for 10 min. As controls, we spotted each donor or recipient cells separately on filter membranes, which were separately placed onto LB agar plate containing Rif and incubated at 30ºC for 10 min.

extract_protocol: The cells were released from the filter by voltexing in 1 mL of RNAprotect Bacteria Reagent (Qiagen), and the total RNA was extracted and purified using RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction. The total RNA was treated by TURBO DNase (Ambion) at 37˚C for 30 min, and purified by RNeasy Cleanup kit (Qiagen). The integrity of RNA samples was checked using 2100 Bioanalyzer (Agilent).

tag: accession


title: 6694 c2 Kdm2a KO c5 [SY2]

tag: cell type


title: SAMPLE 15: Mixture of RNA samples from RifR donor and RifS recipient replicate 1

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifR donor and RifS recipient, respectively.  It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2440, RNA extracted separately


title: SAMPLE 14: Mixture of RNA samples from RifS donor and RifR recipient replicate 2

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifS donor and RifR recipient, respectively.  It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2442, RNA extracted separately


title: SAMPLE 13: RNA sample from conjugation between RifS donor and RifS recipient replicate 2

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifS donor and RifS recipient. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2440, conjugation


title: Volunteer 10

city: Nanjing

first: Jiayang

last: Wu

address: No. 24 Tongjia Lane, Gulou District

institute: China Pharmaceutical University

description: human_whole blood _20

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis.

source_name: whole blood from healthy volunteer

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard protocol  of WT Terminal Labeling and Controls Kit (Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: gender

tag: age

tag: disease state

value: healthy volunteer

value: whole blood


title: input DNA Dicer2 kd rescue CHARRs H3K9me3

value: input

tag: chip antibody


title: Volunteer 09

description: human_whole blood _19

value: male

tag: tissue


title: SAMPLE 11: Mixture of RNA samples from RifR donor and RifR recipient replicate 2

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifR donor and RifR recipient, respectively.  It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2442, RNA extracted separately

tag: genotype


title: Volunteer 06

description: human_whole blood _16


title: SAMPLE 12: Mixture of RNA samples from RifR donor and RifR recipient replicate 1

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifR donor and RifR recipient, respectively.  It is the first of two biological replicates used in this experiment, each from separate cultures.

value: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2442


title: Volunteer 08

description: human_whole blood _18


title: 6694 c2 WT [SY1]

value: wildtype

value: Pancreatic cancer cells


title: Volunteer 02

description: human_whole blood _12


title: Volunteer 03

description: human_whole blood _13


title: input DNA Dicer2 kd rescue CHARRs H3K27me3

value: Dicer2 kd rescue CHARRs


title: Volunteer 04

description: human_whole blood _14


title: D10-RNA-seq

city: Seoul

first: Jaeyeaon

last: Cho

address: 50-1 Yonsei-ro, Seodaemoon-gu

country: South Korea

institute: Yonsei University

description: fibroblasts 10 days after the reprogramming treatment

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v1.14.0 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values using CuffDiff for each Samples

source_name: fibroblasts

growth_protocol: (fibroblast culture) Tail-tip fibroblasts isolated C57BL/6 were expanded in vitro in DMEMF/12 containing 10% FBS

extract_protocol:
Total RNAs were extracted using Rneasy plus kit 0, 6, 10 days after the reprogramming treatments.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (fiboblast reprogramming) fibroblasts plated at 70-80% of confluence were treated with miRNAs, ascorbic acid and BMP4

tag: strain

tag: origin

value: tail-tip fibroblasts


title: input DNA Dicer2 kd rescue CHARRs H3K4me3

value: S2 cells


title: D0_RNA-seq

description: fibroblasts before the reprogramming treatment


title: Volunteer 07

description: human_whole blood _17


title: D6_RNA-seq

description: fibroblasts 6 days after the reprogramming treatment


title: input DNA Dicer2 kd rescue Scramble H3K9me3

value: Dicer2 kd rescue Scramble


title: SAMPLE 9: RNA sample from conjugation between RifS donor and RifR recipient replicate 1

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifS donor and RifR recipient. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2442, conjugation


title: input DNA Dicer2 kd rescue Scramble H3K27me3


title: SAMPLE 8: RNA sample from conjugation between RifR donor and RifR recipient replicate 1

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifR donor and RifR recipient. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2442, conjugation


title: input DNA Dicer2 kd rescue Scramble H3K4me3


title: SAMPLE 10: Mixture of RNA samples from RifS donor and RifS recipient replicate 2

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifS donor and RifS recipient, respectively.  It is the second of two biological replicates used in this experiment, each from separate cultures.

value: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2440


title: Co-culture condition(treated) #3

city: NEW HAVEN

first: Michael

last: Nathanson

state: CONNECTICUT

address: 300 Cedar Street, TAC, S230

department: Internal medicine

institute: Yale university

data_processing:
RNA integrity number was determined by Agilent Bioanalyzer 2100(AgilentTechnologies). On average, 40 million sequencing reads (100 bp paired end) of each sample were obtained using an Illumina 6000 Sequencer. To analyze the sequencing data, we used the public server at usegalaxy.org. The reads were mapped to the University of California Santa Cruz hg19 human genome by STAR (Galaxy Version 2.6.0b-1), 78.62% of which were uniquely aligned to the reference. The raw read counts of genes were counted by feature Counts (Galaxy Version 1.6.4+galaxy1) and the differential expression analysis was conducted by DESeq2 (Galaxy Version 2.11.40.6).
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized values

source_name: Normal Human Cholangiocytes

growth_protocol: Normal Human Cholangiocytes cells were routinely generated by plating 2 days adherent cultures (typically 2.5 × 10^5 cells into 6 well plate) on collagen coated plastic in supecial medium (DMEM F-12 Ham + GlutaMax, MEM Nonessential Amino Acids, Chemically Defined Lipid Conc., MEM Vitamin solution, Soybean Trypsin Inhibitor, Insulin/Transferrin/Selenium-S, Fetal Bovine Serum, Pen/Strep, EGF, Dexamethasone, 3,3'5-triiodo-L-thyronine, Forskolin).

extract_protocol: RNA was expracted according to RNeasy Mini Kit: Qiagen CatNo: 74104.

treatment_protocol: Peripheral venous blood samples approximately 15-20 ml were collected into K2 EDTA tubes (Becton, Dickinson and Co.,Franklin Lakes, NJ) from human, who were not taking any medication. We isolated and purified human neutrophils by density gradient centrifugation using PolymorphPrep (Axis Shield PoC AS, Oslo, Norway) according to the manufacturer's instructions. Briefly, an equal volume of blood was layered over PolymorphPrep solution and was then centrifuged at 500xg for 35 min at 20ºC without the brake. After centrifugation, the polymorphonuclear neutrophil layer was collected and washed with diluted HEPES-buffered saline (1 volume of water and 1 volume of Hank's balanced salt solution (HBSS) to eliminate residues of PolymorphPrep. PMNs were harvested by centrifugation at 400xg for 10 minutes. To purify neutrophils and remove any residual erythrocyte contamination of the granulocyte from the residual red blood cells, cells were washed with ACK lysing buffer (Lonza) and incubated for 7 minutes at 37ºC. Neutrophils were harvested by centrifugation and resuspended in NHC cell medium. Cell density was quantified using a hemocytometer. Purity of neutrophil preparations was confirmed by a cytospin on the isolated neutrophils followed by Wright's or May-Grünwald-Giemsa staining/Pappenheim staining. Then, we co-cultured with Normal human cholangiocytes and isolated neutrophils.

value: cholangiocytes

tag: treatment

value: co-cultured with neutrophils


title: SAMPLE 7: Mixture of RNA samples from RifS donor and RifR recipient replicate 1

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifS donor and RifR recipient, respectively.  It is the first of two biological replicates used in this experiment, each from separate cultures.

value: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2442


title: SAMPLE 6: RNA sample from conjugation between RifS donor and RifS recipient replicate 1

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifS donor and RifS recipient. It is the first of two biological replicates used in this experiment, each from separate cultures.


title: input DNA Dicer2 kd H3K9me3

tag: antibody

value: Dicer2 kd


title: Patient 10

description: human_whole blood _10

source_name: whole blood from human with atherosclerosis-induced ischemic stroke

value: atherosclerosis-induced ischemic stroke


title: Co-culture condition(treated) #2


title: Patient 09

description: human_whole blood _09

value: female


title: Volunteer 01

description: human_whole blood _11

value: healthy volunteer

value: whole blood


title: Patient 08

description: human_whole blood _08

value: male


title: input DNA Dicer2 kd H3K27me3

source_name: S2 cells

value: input

tag: cell line


title: Co-culture condition(treated) #1


title: Co-culture condition(treated) #4


title: input DNA NC H3K9me3

value: NC

tag: passages


title: Non co-culture condition(ctrl) #2

value: control


title: Patient 06

description: human_whole blood _06


title: Dam-Emerin_ZKSCAN3 defecient hMSCs_1

description:
DamID sequencing of ZKSCAN3 deficient hMSCs.
ZK3_P10_EMDvsDam_bin10.bw

source_name: Mesenchymal stem cell

value: Mesenchymal stem cell

value: ZKSCAN3 defecient hMSCs

tag: passage

tag: dam-tagged protein

value: Dam-Emerin


title: SAMPLE 4: RNA sample from conjugation between RifR donor and RifS recipient replicate 1

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifR donor and RifS recipient. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2440, conjugation


title: SAMPLE 5: RNA sample from conjugation between RifR donor and RifS recipient replicate 2

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifR donor and RifS recipient. It is the second of two biological replicates used in this experiment, each from separate cultures.

value: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2440


title: input DNA Dicer2 kd H3K4me3

tag: genotype/variation

value: S2 cells


title: SAMPLE 3: RNA sample from conjugation between RifR donor and RifR recipient replicate 2

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifR donor and RifR recipient. It is the second of two biological replicates used in this experiment, each from separate cultures.

value: Pseudomonas putida KT2442(RP4) and Pseudomonas putida KT2442

tag: accession


title: SAMPLE 2: Mixture of RNA samples from RifR donor and RifS recipient replicate 2

description: This sample is of mixture of samples  from Pseudomonas putida KT2440(RP4) RifR donor and RifS recipient, respectively.  It is the second of two biological replicates used in this experiment, each from separate cultures.


title: Non co-culture condition(ctrl) #1

tag: cell type

value: cholangiocytes


title: input DNA NC H3K4me3 and H3K27me3


title: SAMPLE 1: RNA sample from conjugation between RifS donor and RifR recipient replicate 2

description: This sample is of conjugating mixture between Pseudomonas putida KT2440(RP4) RifS donor and RifR recipient. It is the second of two biological replicates used in this experiment, each from separate cultures.

value: Pseudomonas putida KT2440(RP4) and Pseudomonas putida KT2442


title: ZFP36_input-2

status: Public on Mar 12 2020

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
ZFP36_IP_1_peak_info.txt
ZFP36_IP_2_peak_info.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of ZFP36 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HeLa cell

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from ZFP36-RNA complexes and another for the western blotting assay for ZFP36 immunoprecipitation.The ZFP36-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

value: HeLa Cell line


title: ZFP36_IP-2

value: TTP


title: ZFP36_IP-1


title: Non co-culture condition(ctrl) #3


title: ZFP36_input-1


title: Patient 07

description: human_whole blood _07

tag: gender

value: atherosclerosis-induced ischemic stroke


title: Patient 05

description: human_whole blood _05

tag: age


title: Patient 03

description: human_whole blood _03

value: female

tag: disease state


title: PAECS_replicate_1

city: Heidelberg

first: Judith

middle: B

last: Zaugg

state: Heidelberg

address: Meyerhofstraße 1

institute: European Molecular Biology Laboratory (EMBL)

description: CTCF ChIA-PET in human pulmonary artery endothelial cell

data_processing:
Library strategy: ChIA-PET
We used the general Mango workflow which can be divided into these main steps:
Step 1 consists to remove linkers from reads and filtering reads based on the combination of linkers. Only PETs with the identical linker sequences at both ends will be kept.
Step 2, reads were aligned to the hg19 genome using Bowtie.
Step 3, we removed reads that may be due to polymerase chain reaction duplication and organizes the data for peak calling and interaction analysis.
Step 4, we made peak calling using MACS2 to call binding peaks, that will be subsequently used as anchor points for the detection of interactions in step 5 (Zhang et al., 2008).
Step 5, statistical confidence estimates are assigned to interactions based on comparison to a model that considers both genomic distance and the read depth of each peak. The resulting P values are corrected to account for multiple hypothesis testing and filtered to a user defined false discovery rate (FDR) for 10% of FDR.
Genome_build: hg19
Supplementary_files_format_and_content: pairs of interactions between genomic regions

source_name: Homo sapiens pulmonary artery endothelial primary cell

extract_protocol:
Fixation: Cells were crosslinked with formaldehyde at a final concentration of 1% for 10 minutes at room temperature. The reaction was quenched with Glycine at a final concentration of 125mM and nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals).
ChIA-PET protocol: We followed the published protocol by (Heidari et al., 2014) with modifications as described in detail here. Briefly, cells were crosslinked and subjected to nuclear lysis followed by chromatin shearing. Immunoprecipitation was performed overnight at 4 °C with antibodies against the CTCF. The antibody used for ChIA-PET is CTCF (Cell signaling technology [#3418]). The immuno-complexes were pulled down with Protein-G dynabeads (Lifetechnologies #10003D, New York). Biotinylated linkers were ligated to the enriched fragments, followed by proximity ligation overnight at 16 °C. Crosslinking was reversed at 65 °C with use of Proteinase K followed by DNA purification. DNA fragments were tagmented with Illumina nextera transposase. After Streptavidin pull-down fragments were amplified using PCR and subjected to Illumina sequencing.

value: CTCF

tag: assay

value: ChIA-PET

value: primary cell


title: PAECS_replicate_2

value: pulmonary artery endothelial primary cell


title: Patient 04

description: human_whole blood _04

value: male

tag: tissue

value: whole blood


title: KD_H3K27ac_ChIPSeq

city: tianjin

first: Yongqiang

last: Hou

address: No. 22 Qixiangtai Road, Heping District, Tianjin

institute: Tianjin Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
The high quality reads were mapped to the Human genome of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed."
Peak calling were performed using MACS version 1.4.2
Genome_build: GRCh37
Supplementary_files_format_and_content: bw files were generated using MACS

source_name: MDA-MB-231 cell

growth_protocol: MDA-MB-231 cells were cultured in L-15 medium supplemented with 10% FBS and without CO2.

extract_protocol:
Approximately 5 x 10^7 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibodies against PHF20L1, EZH2, MTA1, H3K27me2, H3K27me3 or H3K27ac. The DNA was purified with a Qiagen PCR purification kit
A Vazyme TruePrep DNA Library Prep Kit V2 for Illumina ® (Vazyme Biotech) was used for DNA library construction. Briefly,the kit uses a new-type transposasea for DNA fragmentation and ligation  of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Transfections with siRNA against PHF20L1 were performed using Lipofectamine 2000® or Lipofectamine RNAiMAX® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions

value: PHF20L1 knockdown

tag: chip antibody


title: Patient 02

description: human_whole blood _02


title: KD_H3K27me3_ChIPSeq

value: anti-H3K27me3 (Cell Signaling Technology, #9733, rev.01/30/17)


title: CLL_A_del17p_untreated_2

city: Ulm

first: Deyan

last: Yosifov

address: Albert-Einstein-Allee 23

institute: University Hospital Ulm

data_processing: The raw data were processed using the RnBeads package in R/Bioconductor. Probes known to be cross-reactive (43 230) or overlapping known single-nucleotide polymorphisms (SNPs; 8 704), as well as probes giving unreliable measurements (884 as determined by the Greedycut algorithm) were excluded from analysis. The data from the remaining 432 759 probes were subjected to background subtraction using the Noob method and beta-mixture quantile normalization (BMIQ). This normalization strategy successfully mitigated the inherent bias in β-value distributions between the two different types of probes (Infinium I and II) that are present on the HumanMethylation450 BeadChip. In a subsequent step, probes of non-CpG context (1 251), probes binding to sequences on sex chromosomes (9 917) and probes with low standard deviation (69 867) were filtered out. The data obtained by the remaining 351 724 probes were used in downstream analyses.

source_name: CLL, group A (del(17p) and/or TP53mut, untreated)

extract_protocol: Genomic DNA was extracted from CD19+ fractions of patients' peripheral blood mononuclear cells (PBMCs) using Qiagen AllPrep Kit according to standard instructions

tag: Sex

value: unknown

tag: treated

value: no

tag: response to therapy

value: not applicable

value: unmutated

value: yes

value: missense


title: ATAC-seq_ZKSCAN3 defecient hMSCs_3

description:
ATAC sequencing of ZKSCAN3 deficient hMSCs.
ZK3_bin10_extend_250.bw

value: Mesenchymal stem cell

tag: genotype

value: ZKSCAN3 defecient hMSCs


title: KD_H3K27me2_ChIPSeq

tag: cell line


title: KD_MTA1_ChIPSeq

value: anti-MTA1 (Cell Signaling Technology, Cat#5647, lot#2)


title: Normal-MTA1-ChIPSeq

value: control


title: Normal_H3K27ac_ChIPSeq


title: Normal_H3K27me3_ChIPSeq


title: input DNA


title: Normal-PHF20L1-ChIPSeq

value: anti-PHF20L1 (Sigma-Aldrich, HPA028417, A8319)


title: KD_EZH2_ChIPSeq

value: anti-EZH2 (Becton Dickinson, Cat.#612667, lot# 2326715)


title: Normal_H3K27me2_ChIPSeq


title: Normal-EZH2-ChIPSeq


title: H3K4me3_PAH9_female_wild type_2

data_processing:
Illumina adapters were trimmed with Trimmomatic V0.33 using paired-end mode and with these parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Reads of 100 bp in length were aligned to the human genome assembly (hg19) with the Burrows–Wheeler Aligner (version: 0.6.1) (Li and Durbin, 2009) by bwa and later bwa SAMPE. SAM files were transformed into BAM files and using SAMtools we filtered-out non-uniquely mapped reads and mapped reads to mitochondrial chromosome. Finally, we removed duplicated reads using Piccard (picard-tools-1.119). BAM files with higher library size than the median across samples were downsampled for each assay.
Fragment length of each library using were estimated using ChIPQC R/Bioconductor package (Carroll et al., 2014).
Peak calling was carried out for each downsampled ChIP-seq data in MACS2 (version: macs2-2.1.0.20150731, using the following parameters  --nomodel --extsize [estimated for each library] --pvalue 0.01).
Blacklisted regions (available at wgEncodeDacMapabilityConsensusExcludable.bed) that are excludable for hg19 in ChIP-seq experiments were removed using BEDtools.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: pulmonary arterial endothelial cells

extract_protocol:
Briefly, Cells were cross-linked with formaldehyde for 10 minutes (final concentration of 1%). Chromatin Immunoprecipitation was carried out for about 20 millio cells using antibodies against H3K27ac, H3K4me1, or H3K4me3. In more detail, chromatin immunoprecipitation followed by massively parallel sequencing was carried out as previously described (Kasowski et al., 2013).
Illumina TruSeq library preparation was used for preparing the libraries of enriched fragments and finally subjected to paired-end sequencing.

tag: antibody

tag: condition

value: PAH

value: female

value: wild type

tag: batch


title: H3K4me3_PAH7_female_wild type_1


title: Patient 01

description: human_whole blood _01

value: atherosclerosis-induced ischemic stroke

value: whole blood


title: H3K4me3_PAH6_female_wild type_1


title: H3K4me3_PAH3_female_BMPR2_1


title: H3K4me3_PAH4_male_wild type_1

value: male


title: H3K4me3_PAH5_male_wild type_2


title: H3K4me3_PAH2_male_BMPR2_1


title: H3K4me3_PAH10_female_wild type_1


title: H3K4me3_CTRL6_male_wild type_1

value: CTRL


title: H3K4me3_CTRL7_female_wild type_2


title: H3K4me3_CTRL5_male_wild type_1


title: H3K4me3_PAH1_female_wild type_1


title: H3K4me3_CTRL9_male_wild type_2


title: H3K4me3_CTRL4_female_wild type_1


title: H3K4me3_CTRL2_female_wild type_1


title: H3K4me1_PAH9_female_wild type_2


title: H3K4me1_PAH5_male_wild type_2


title: H3K4me1_PAH6_female_wild type_1


title: H3K4me1_PAH8_male_wild type_1


title: H3K4me1_PAH3_female_BMPR2_2


title: H3K4me1_PAH7_female_wild type_1


title: H3K4me1_CTRL9_male_wild type_2


title: H3K4me1_PAH1_female_wild type_1


title: H3K4me3_PAH8_male_wild type_1


title: H3K4me1_CTRL8_female_wild type_2


title: H3K4me3_CTRL8_female_wild type_2


title: H3K4me1_PAH10_female_wild type_1


title: H3K4me1_CTRL5_male_wild type_1


title: H3K4me1_CTRL4_female_wild type_1


title: H3K4me3_CTRL3_male_wild type_1


title: H3K4me1_CTRL2_female_wild type_1


title: H3K4me1_PAH4_male_wild type_1


title: H3K4me1_CTRL3_male_wild type_1


title: H3K4me1_PAH2_male_BMPR2_1


title: H3K4me1_CTRL10_male_wild type_2


title: H3K27ac_PAH9_female_wild type_2


title: Exhaust

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
Raw reads (fastq files) were aligned to mouse reference (mm10) using STAR aligner (version 2.6) with default settings, read count files were generated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text for gene read count, sample information, and gene annotation

source_name: Splenocytes

extract_protocol:
TEa cells were sorted,  flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Samples were then sent to Novogene Inc. (Sacramento, CA) for low-input Total RNA library construction using the SMRTER kit lib (Takara Inc. Mountain View, CA)

tag: strain

value: TEa cells

tag: treatment

value: Adoptively transferred into CB6F1 mice


title: H3K4me3_CTRL10_male_wild type_2


title: H1975–OR cells, 1,25(OH)2D3+Osimertinib, 5c

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference (p10) ENSEMBL annotation v91 using STAR_2.5.2b
Reads counts are obtained using Kallisto v0.43.0
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Lung adenocarcinoma

growth_protocol: Cells were cultured in cultured in RPMI 1640  supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. H1975-OR cells were cultured as above with the addition of 500nM osimertinib

extract_protocol:
Cells were lysed in TRI-reagent and RNA isolated using Direct-zol RNA miniprep kit
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold kit.

tag: egfr status

value: Osimertinib resistant


title: H1975–OR cells, 1,25(OH)2D3+Osimertinib, 5b


title: Effector

tag: cell type

value: Adoptively transferred into WT C57BL/6 recipients receiving Balb/c skin transplant


title: H1975–OR cells, Osimertinib, 4c

value: Osimertinib


title: H3K27ac_PAH4_male_wild type_1

tag: gender


title: H3K27ac_PAH6_female_wild type_1


title: H3K27ac_PAH8_male_wild type_1


title: H3K27ac_PAH3_female_BMPR2_2


title: H1975–OR cells, 1,25(OH)2D3+Osimertinib, 5a


title: H3K27ac_PAH7_female_wild type_1


title: H3K27ac_PAH2_male_BMPR2_1


title: Volunteer 05

description: human_whole blood _15

source_name: whole blood from healthy volunteer

tag: age

tag: disease state

value: healthy volunteer


title: H1975–OR cells, Osimertinib, 4a


title: H3K27ac_PAH10_female_wild type_1


title: H1975–OR cells, Osimertinib, 4b


title: cell-knock out-rep1

city: xinxiang

first: xiaofeng

last: zhou

address: No. 601 Jinsui Avenue

institute: xinxiang medical university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cell lines were cultured in RPMI 1640 Medium containing 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted with RNeasy Plus Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s specifications.

treatment_protocol: The PARK2 sgRNA was designed, synthesized, and cloned to the pX460 cloning vectors. Then, 100 million ESCC cells were electroporated with 4 μg of pX460 plasmid containing sgRNA using the Nucleofector™ 2b Device (Lonza). After the electroporation, cell population was sorted by flow cytometry


title: H3K27ac_PAH1_female_wild type_1


title: cell-knock out-rep2


title: cell-wild type-rep1


title: H3K27ac_CTRL8_male_wild type_2


title: cell-wild type-rep2


title: cell-knock out-rep3


title: H1975–OR cells, 1,25(OH)2D3, 3c


title: cell-wild type-rep3


title: H3K27ac_CTRL7_female_wild type_2


title: H1975–OR cells, 1,25(OH)2D3, 3a


title: H3K27ac_PAH5_male_wild type_2


title: H1975–OR cells, Vehicle, 2c

value: Vehicle


title: H3K27ac_CTRL5_male_wild type_1


title: H1975–OR cells, Vehicle, 2b


title: H3K27ac_CTRL4_female_wild type_1


title: H1975–OR cells, Vehicle, 2a


title: H1975 cells, Vehicle, 1c

value: Parental


title: H3K27ac_CTRL3_male_wild type_2


title: H3K27ac_CTRL2_female_wild type_1


title: H1975–OR cells, 1,25(OH)2D3, 3b


title: H1975 cells, Vehicle, 1a


title: H1975 cells, Vehicle, 1b


title: Patient derived pancreatic cancer organoids  p53R175H OFF shRNA2 Replicate 3

city: New York

first: Xiaoli

last: Mi

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq read mapping. For a robust analysis of subtle expression and splicing effects, alignment-based and alignment-free methods were combined. Reads were aligned to Gencode annotation v25 for human or vM12 for mouse using STAR v2.4.1d and quantified by QoRTs v1.1.8, while alignment-free quantification was performed by Kallisto v0.43.0 accounting for hexamer bias and using 100 bootstrap iterations to quantify the technical uncertainty.
Differential gene expression and isoform expression measurements. Differentially expressed genes were then identified from aligned data by DESeq2 v1.10.18 and from alignment-free data by Sleuth v0.28.1. Isoform expression measurements were identified from aligned data by MISO v0.5.3 and from alignment-free data by SUPPA v1. These two algorithms take complementary approaches. While MISO uses the number of split reads aligning to nearby exon junctions to calculate the percent spliced in (PSI) value and a Bayes factor for each splicing event (cassette exon etc.). SUPPA extracts the PSI values for known splicing defects from transcript quantification. Statistical significance is then calculated using a Kolmogorov-Smirnov test to compare the PSI distributions of two conditions as a function of the expression of the transcripts defining the events. To further validate the significance of the splicing defects, the empirical version of the SUPPA algorithm was applied to samples permuted in such to eliminate any biological effect.
Genome_build: Reads were aligned to Gencode annotation v25 for human or vM12 for mouse using STAR v2.4.1d and quantified by QoRTs v1.1.8, while alignment-free quantification was performed by Kallisto v0.43.0 accounting for hexamer bias and using 100 bootstrap iterations to quantify the technical uncertainty.

source_name: organoids

growth_protocol: Primary patient derived and murine PanIN organoids were culture following the protocols previously described5. Murine PDAC cells (KrasG12D; p53R172H/null; Pdx1-Cre [KPC cells]) and 293T cells, were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% Pen Strep (Gibco). All cell lines were incubated at 37°C and 5% CO2. Primary patient derived organoids were generated at Memorial Sloan Kettering Cancer Center (MSKCC) using primary patient samples from tumor resection under Institutional Review Boards approval and in accordance to the Declaration of Helsinki protocol. Informed consents were obtained from all human subjects. Murine PanIN organoids were generated using the Mist1:CreERT2 (CiMist1) Lox-Stop-Lox (LSL)-KrasG12D/+ mice6 with td Tomato tracer and following the protocol from Boj et al., 20155. Murine PDAC cells were obtained from Dr. Robert Vonderheide, generated from the PDX-1-Cre; LSL-KrasG12D/+; LSL-Trp53R172H/+7. All cells are tested yearly for mycoplasma contamination.

extract_protocol:
For all cells, RNA was extracted using Qiagen RNeasy columns.
poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5× AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1× beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose). 300 bp DNA fragments were isolated and sequenced on the Illumina HiSeq 2000 (~100M 2×49 bp reads per sample).

value: organoids


title: H3K27ac_CTRL6_male_wild type_1


title: Patient derived pancreatic cancer organoids  p53R175H OFF shRNA1 Replicate 3


title: Patient derived pancreatic cancer organoids  p53R175H OFF shRNA2 Replicate 2


title: lib18824: CAT-EEC 552170

city: Bethesda

first: Tielin

last: Qin

state: MD

address: 7500 Old Georgetown Road, Suite 800

institute: Immune Tolerance Network

description: processed data file: P197-1_CB6GMANXX_171009_combined_counts.csv

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: GRCh38 release 77
Supplementary_files_format_and_content: P197-1_CB7GFANXX_170912_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.
Supplementary_files_format_and_content: P197-1_CB6GMANXX_171009_combined_counts.csv is a comma separated value file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

molecule: polyA RNA

source_name: Nasal RNA

extract_protocol:
RNA easy kit, Thaw samples at RT. Vortex. Pass 700ul through Qiashredder. Most tubes contain 2x 700ul, collect flow through in  5ml Eppendorf tubes. Add equal volume of 70% EtOH, mix, transfer 700ul to elute columns.
sequencing libraries were constructed from total RNA using TruSeq stranded mRNA library kit

tag: tissue

value: Nasal RNA

tag: participantid

tag: visitnumber

tag: barcode

tag: randomized treatment

value: Group A (NAC followed by EEC)

value: Male

tag: race

value: White/Caucasian


title: lib18823: CAT-EEC 659498

tag: Sex

value: Female

value: Black or African American


title: Patient derived pancreatic cancer organoids  p53R175H OFF shRNA2 Replicate 1


title: Patient derived pancreatic cancer organoids  p53R175H OFF shRNA1 Replicate 1


title: lib18821: CAT-EEC 444825


title: Patient derived pancreatic cancer organoids  p53R175H OFF shRNA1 Replicate 2


title: Patient derived pancreatic cancer organoids  p53R175H ON Replicate 3


title: lib18825: CAT-EEC 766909

value: Group B (EEC followed by NAC)


title: Patient derived pancreatic cancer organoids  p53R175H ON Replicate 1


title: lib18819: CAT-EEC 444898


title: lib18822: CAT-EEC 874241


title: lib18818: CAT-EEC 122809


title: lib18820: CAT-EEC 766905


title: Npy Rep3

city: Dallas

first: Li

last: Li

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

data_processing:
Mapping: Genome MM10 assembly using HISAT2
Differnental expression analysis was preformed in Bioconductor version 3.8 packages rSamtools, edgeR version 3.8. Values are expressed as transcripts per million mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: Hypothalamus

extract_protocol:
1 ng of total RNA
SMARTer® Stranded Total RNA-Seq Kit v2

treatment_protocol: Arcuate nuclei were dissected. Neurons were dissassociated

tag: embryonic age (days)

tag: neuron type

value: Npy


title: Npy Rep2


title: lib18817: CAT-EEC 874171

value: Other


title: Patient derived pancreatic cancer organoids  p53R175H ON Replicate 2


title: lib18816: CAT-EEC 444834


title: H3K4me1_CTRL6_male_wild type_1

tag: antibody

tag: condition

value: CTRL

value: male

value: wild type

tag: batch


title: lib18815: CAT-EEC 337498


title: Npy Rep1


title: Pomc Rep 4

value: Pomc


title: lib18814: CAT-EEC 176553


title: H3K4me1_CTRL7_female_wild type_1

value: female


title: Pomc Rep 3


title: Sample52 hESC hESC Location:whole but could be disorganized Cultured:RetinalOrganoid H9

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: Illumina protocol

source_name: hESC

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Following the desulphonation and wash steps, converted DNA was eluted in 12 μl of the M-Elution buffer and then loaded onto the Infinium Human Methylation 450K BeadChip kit (Illumina, #WG-314-1003)

extract_protocol: Genomic DNA of the retinas was precipitated from the interphase and phenol  phase of the TRIzol solution using 100% ethanol. The DNA pellet was washed 3 times  with 0.1 M sodium citrate/10% ethanol solution and once with 75% ethanol. The pellet  was then resuspended in 8 mM NaOH buffer or concentrated using gDNA Clean and  Concentrator kit (Zymo Research, Irvine, CA).

tag: basename

tag: detailed location retina

value: whole but could be disorganized

tag: culture method

value: RetinalOrganoid

tag: externalsampleid

value: H9_20d (RNAseq)

tag: humanid

tag: gestational day

tag: days in vitro

tag: human expected days


title: Pomc Rep 2


title: lib18812: CAT-EEC 659618

tag: tissue

value: Nasal RNA

tag: participantid

tag: visitnumber

tag: barcode

tag: age


title: Sample45 Human Fetal retina Location:whole Cultured:NotCultured H27482

source_name: Human fetal retina

value: whole

value: NotCultured

value: 136d_T21 (RNAseq)

tag: Sex


title: lib18813: CAT-EEC 498493

tag: randomized treatment

value: Group A (NAC followed by EEC)

value: Female

tag: race

value: White/Caucasian


title: Pomc Rep 1

tag: embryonic age (days)

tag: neuron type


title: Sample49 Human Fetal retina Location:whole Cultured:Explant H27446

tag: batch

tag: basename

tag: detailed location retina

value: Explant

value: 59d_Control_6wks (SC-RNAseq)

value: Male


title: Sample47 Human Fetal retina Location:whole Cultured:NotCultured H27427

tag: culture method

tag: externalsampleid

value: 89d_T21 (RNAseq)

tag: humanid


title: Sample50 Human Fetal retina Location:whole Cultured:Explant H27447

tag: gestational day

tag: days in vitro

tag: human expected days


title: lib18811: CAT-EEC 337562

tag: tissue

tag: participantid

tag: visitnumber

value: Group B (EEC followed by NAC)


title: Sample46 Human Fetal retina Location:whole Cultured:NotCultured H27508

value: 110d_T21 (RNAseq)

tag: Sex


title: Sample51 Human Fetal retina Location:whole Cultured:Explant H27468


title: Sample53 hESC hESC Location:whole but could be disorganized Cultured:RetinalOrganoid H9

value: H9_30d (RNAseq)


title: lib18810: CAT-EEC 766873

tag: barcode

tag: randomized treatment

tag: age


title: Sample54 hESC hESC Location:whole but could be disorganized Cultured:RetinalOrganoid H9

value: whole but could be disorganized

value: H9_40d (RNAseq)


title: Sample44 Human Fetal retina Location:whole Cultured:NotCultured H27476

value: 113d_T21 retina (RNAseq)


title: Sample38 Human Fetal retina Location:whole Cultured:NotCultured H-26723


title: Sample43 Human Fetal retina Location:Periphery Cultured:NotCultured H-26930

value: Periphery


title: siPHF20L1#3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were aligned to the reference genome using Tophat v2.1.1
Transcript abundance was quantified using the htseq-count script in the Python package HTSeq v0.6.0.
Genome_build: GRCh37

extract_protocol:
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library Prep Kit with standard Illumina protocols

tag: cell line

tag: genotype/variation

value: PHF20L1 knockdown


title: Sample40 Human Fetal retina Location:whole Cultured:Explant H-26992

tag: batch

tag: basename

value: whole

value: SampleDay115 + 0 DIVExplantsInPairsH-26992 Ctl to 21DIV


title: Sample41 Human Fetal retina Location:OpticNerve Cultured:NotCultured H-26930

tag: detailed location retina

value: OpticNerve

tag: culture method

value: NotCultured


title: siControl#3

value: control


title: Sample36 Human Fetal retina Location:whole Cultured:Explant H-27138

value: Explant

tag: externalsampleid

value: SampleDay115 + 0 DIVExplantsInPairsH-27138

tag: humanid

value: Female


title: lib18841: CAT-EEC 391157

description: processed data file: P197-1_CB7GFANXX_170912_combined_counts.csv

value: Nasal RNA

value: Male

tag: race

value: Asian


title: Sample42 Human Fetal retina Location:Periphery Cultured:NotCultured H-26877

value: SampleDay84 #6 Rest of peripherySubdividedRetinaH-26877

value: Unknown

tag: gestational day

tag: days in vitro

tag: human expected days


title: Sample48 Human Fetal retina Location:whole Cultured:Explant H27426


title: Sample39 Human Fetal retina Location:whole Cultured:Explant H-26973

value: Sample105+0DIV ExplantsInPairs(Round2)


title: lib18840: CAT-EEC 230161

tag: tissue

tag: participantid

tag: visitnumber

value: Group B (EEC followed by NAC)


title: Sample37 Human Fetal retina Location:whole Cultured:Explant H27138

tag: Sex


title: Sample31 Human Fetal retina Location:whole Cultured:Explant H-27179


title: Sample34 Human Fetal retina Location:whole Cultured:Explant H27139

value: SampleDay94 + 0DIVExplantsInPairsH27139 F


title: siPHF20L1#2

value: PHF20L1 knockdown