title: Pilot experiment, 2 sgRNAs, sgRNA

description:
10x Genomics Feature Barcode for CRISPR screening library, single index
BUT290A1_BUT290A2_matrix.mtx.gz
BUT290A1_BUT290A2_barcodes.tsv.gz
BUT290A1_BUT290A2_features.tsv.gz

value: CRISPR sgRNA


title: donor6_biorepl1_spikein_10pRNA_W1

status: Public on Jul 11 2023

type: SRA

city: Seattle

first: Asia

last: Mendelevich

state: WA

address: 2211 Elliott Ave

country: USA

institute: Altius

description:
donor no. 6 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 6 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

library_source: transcriptomic

data_processing:
Sequence reads were aligned on two alellic pseudogenomes using STAR v2.7.9a (with parameters –outSAMattributes vA vG).
Uniquely aligned reads were assigned towards one of the alleles according to their SNP calls and alignment quality (see https://github.com/gimelbrantlab/fastq2allelictabs).
Allelic gene counts were calculated using featurecounts v2.0.2.
Supplementary files format and content: Tab-delimited text files include allelic gene count values for each sample.

molecule: polyA RNA

organism:
Caenorhabditis elegans
Homo sapiens

source_name: peripheral blood monocytes / whole organism

extract_protocol:
Qiagen Mini / Trizol
SMART-Seq v4 PLUS kit (Takara)

tag: cell type

tag: genotype

value: WT

tag: strain

value: donor no. 6 / N2 x Hawaii


title: WT JB4/EI7HZ2 Day 9 Replicate 3, RNA-seq

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

country: Japan

institute: Mie University

description:
mm9
non-haplotype resolved; excluding chrX

data_processing:
The adapter-sequence trimming and removal of low-quality base reads were performed by trim_galore version 0.6.6 (--quality 20 --phred33 --length 35)
Trimmed fastq files were aligned to the mouse genome (UCSC mm9) by tophat2 version 2.1.1.
We removed rRNA reads from the mapped reads and excluded reads from the X chromosome for genome-wide non-haplotype resolved analysis.
Filtered mapped reads were quantified against the annotated UCSC transcriptome for mm9 to calculate FPKM (Fragments per kilobase per million mapped fragments) values using the Cuffdiff program of the Cufflinks. (version 2.2.1)
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: JB4/EI7HZ2 mESCs were grown in serum containing medium + 2i/LIF [MEK and GSK3 inhibitors (2i) and leukemia inhibitory factor (LIF)] (DMEM (Nacalai , 08458-45 500 ml, or sigma, cat#D6429-500ML); 15% FBS (gibco 10270-106, lot# 42Q6272K); 1× Pen/strep (Nacalai, 09367-34); 1× Non-essential amino acid (Nacalai, 06344-56); 0.1 mM β-mercaptoethanol (Gibco, 21985-023); 1000 U/ml LIF (Nacalai USA, NU0012-2); 1 µM PD0325901 (Wako, 162-25291); 3 µM CHIR99021 (Wako, 034-23103)) on culture plate coated with 0.2% gelatin. Medium also contained 0.2 mg/ml G418 (invivogen, ant-gn-1) and 25 µg/mL Zeocin (invivogen, ant-zn-1) in order to maintain two X chromosomes state. Wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs were differentiated to neuroectoderm for 7 or 9 days as described (Miura et al., 2019). Neural stem cells (NSCs) were derived from wild-type and SmcHD1-mutant JB4/EI7HZ2 mESCs and cultured as described (Pollard et al., 2006). NSCs were cultured in NSC maintenance media [(DMEM/F12 (nacalai tesque, #11581-15); 1× N2 supplement (Thermo Fisher, 17502048); 2 mM L-Glutamine (Nacalai tesque, #16948-08); 1× Pen/strep (Nacalai tesque, 09367-34); 75 µg/ml BSA (sigma, A3311-10G); 25 µg/ml Insulin (sigma, I1882-100MG); 10 ng/ml FGF2 (Peprotech 100-18B); 10 ng/ml EGF (Funakoshi, 2028-EG-200)] on 0.2% gelatin coated plate.

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep (ZymoResearch, R2050). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation (96 Samples) (Illumina, 20040534) following manufacturer's protocols.

tag: tissue

value: embryonic stem cell

tag: cell line

value: day-9 differentiated ESCs

tag: Sex

value: female

tag: treatment

value: differentiation to embryoid body


title: WT JB4/EI7HZ2 Day 9 Replicate 2, RNA-seq


title: WT JB4/EI7HZ2 Day 9 Replicate 1, RNA-seq


title: donor1_biorepl1_spikein_10pRNA_W1

description:
donor no. 1 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 1 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: peripheral blood monocytes / whole organism

value: donor no. 1 / N2 x Hawaii


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 3, RNA-seq

value: day-7 differentiated ESCs

value: SmcHD1 knockout


title: mouse2_spleen_chunk1_repl2_spikeinW2

description:
Mouse no.2 (129S1xCAST F1), spleen, with C.elegans (2:1 N2:Hawaii) RNA spike-in, library preparation replicate 2
POLMOT_E2.Mouse_Roundworm.counts.tsv

organism:
Caenorhabditis elegans
Mus musculus

source_name: spleen / whole organism

extract_protocol:
Trizol
NEBNext® Single Cell/Low Input RNA

value: spleen / whole organism

value: 129S1/SvImJ x Cast/EiJ F1 / N2 x Hawaii


title: SmcHD1-KO JB4/EI7HZ2 Day 9 Replicate 1, RNA-seq


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 2, RNA-seq


title: donor2_biorepl1_spikein_10pRNA_W1

description:
donor no. 2 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv

value: donor no. 2 / N2 x Hawaii


title: Healthy control (Group 4, C6)

type: RNA

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

country: Italy

institute: University of Padova

description: miRNA expression profiling of healthy control (Group 4, C6)

hyb_protocol: Probes were hybridized at 55°C for 22 hours using the Agilent's hybridization oven that is suited for bubble-mixing and microarray hybridization processes.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings. Agilent Feature Extraction software version 12.0.0.7 was used for image analysis.

data_processing: Inter-array normalization of miRNA expression levels was performed with cyclic Lowess for miR [Risso et al., 2009] and the average of replicates was used. Feature Extraction software (Agilent Technologies) was used to obtain spot quality measures in order to evaluate the quality and the reliability of the hybridization. In particular, the flag “glsFound” (set to 1 if the spot has an intensity value significantly different from the local background, 0 otherwise) was used to filter out unreliable probes: flag equal to 0 will be noted as “not available” (NA). So, in order to perform a more robust and unbiased statistical analysis, probes with a high proportion of NA values were removed from the dataset. NA (44%) was used as threshold in the filtering process, obtaining a total of 210 available human miRNAs.

organism: Homo sapiens

source_name: Olfactory epithelium cells (OE)

label_protocol: Total RNA (200 ng) was labeled with pCp Cy3, according to the Agilent’s protocol, and unincorporated dyes were removed with MicroBioSpin6 columns (BioRad, Hercules, CA, USA)

extract_protocol: Total RNA, including miRNAs, was extracted from the olfactory epithelium cells by using “Monarch® Total RNA Miniprep kit” (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions. Briefly, this kit is a comprehensive solution for sample preservation, cell lysis, gDNA removal, and purification of total RNA from a wide variety of biological samples, including mammalian tissue. Total RNA was quantified by Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity, and the content of miRNAs (%) in each sample were assessed by capillary electrophoresis with the RNA 6000 Nano LabChip and the Small RNA Nano LabChip, respectively, using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only samples with RNA Integrity Number (R.I.N.) values higher than six were used for gene and miRNA expression analysis.

value: olfactory epithelium


title: SmcHD1-KO JB4/EI7HZ2 Day 7 Replicate 1, RNA-seq


title: mouse2_spleen_chunk1_repl1_spikeinW1

description:
Mouse no.2 (129S1xCAST F1), spleen, with C.elegans (1:1 N2:Hawaii) RNA spike-in, library preparation replicate 1
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: SARS-Cov-2 patient with no olfactory symptoms  (Group 3, P22)

description: miRNA expression profiling of patient with no olfactory symptoms  (Group 3, P22)


title: Healthy control (Group 4, C5)

description: miRNA expression profiling of healthy control (Group 4, C5)


title: mouse1_liver_chunk2_repl2_spikeinW3

description:
Mouse no.1 (129S1xCAST F1), liver, chunk 2, with C.elegans (1:2 N2:Hawaii) RNA spike-in, library preparation replicate 2
POLMOT_E2.Mouse_Roundworm.counts.tsv

source_name: liver / whole organism

value: liver / whole organism


title: M1W1_50vs50_pRNA_repl3

description:
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 50:50 proportion, library preparation replicate 3
LOVSON_E1.Mouse_Roundworm.counts.tsv

source_name: v-Abl pro-B clonal cell line Abl.1 / N2 and Hawaii strains

extract_protocol:
Agilent Mini / Trizol
NEBNext® Single Cell/Low Input RNA

value: pro-B cells / whole organism


title: WT JB4/EI7HZ2 Day 7 Replicate 3, RNA-seq


title: SARS-Cov-2 patient with no olfactory symptoms  (Group 3, P8)

description: miRNA expression profiling of patient with no olfactory symptoms  (Group 3, P8)


title: mouse1_liver_chunk2_repl1_spikeinW1

description:
Mouse no.1 (129S1xCAST F1), liver, chunk 2, with C.elegans (1:1 N2:Hawaii) RNA spike-in, library preparation replicate 1
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: M1W1_50vs50_pRNA_repl2

description:
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 50:50 proportion, library preparation replicate 2
LOVSON_E1.Mouse_Roundworm.counts.tsv

value: v-Abl pro-B clonal cell line Abl.1 / N2 and Hawaii strains


title: WT JB4/EI7HZ2 Day 7 Replicate 2, RNA-seq

value: WT


title: mouse2_liver_chunk1_repl1_spikeinW1

description:
Mouse no.2 (129S1xCAST F1), liver, with C.elegans (1:1 N2:Hawaii) RNA spike-in, library preparation replicate 1
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: mouse1_liver_chunk1_repl1_spikeinW1

description:
Mouse no.1 (129S1xCAST F1), liver, chunk 1, with C.elegans (1:1 N2:Hawaii) RNA spike-in, library preparation replicate 1
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: M1W1_50vs50_pRNA_repl1

description:
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 50:50 proportion, library preparation replicate 1
LOVSON_E1.Mouse_Roundworm.counts.tsv


title: mouse1_liver_chunk1_repl2_spikeinW2

description:
Mouse no.1 (129S1xCAST F1), liver, chunk 1, with C.elegans (2:1 N2:Hawaii) RNA spike-in, library preparation replicate 2
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: H1W1_85vs15_pRNA_repl3

description:
Mix of GM12878.DF1 cell line and C.elegans strains mix (N2:Hawaii) RNA, 85:15 proportion, library preparation replicate 3
LOVSON_E1.Human_Roundworm.counts.tsv

source_name: clonal pro-B cell line GM12878.DF1 / N2 and Hawaii strains

value: GM12878.DF1 / N2 x Hawaii


title: WT JB4/EI7HZ2 Day 7 Replicate 1, RNA-seq

description:
mm9
non-haplotype resolved; excluding chrX

value: embryonic stem cell


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 3, RNA-seq

value: embryonic stem cells


title: SARS-Cov-2 patient with persistent olfactory symptoms  (Group 1, P17)

description: miRNA expression profiling of patient with persistent olfactory symptoms  (Group 1, P17)


title: SARS-Cov-2 patient with no olfactory symptoms  (Group 3, P9)

description: miRNA expression profiling of patient with no olfactory symptoms  (Group 3, P9)


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, RNA-seq

value: female


title: M1W1_27vs73_pRNA_repl3

description:
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 27:73 proportion, library preparation replicate 3
LOVSON_E1.Mouse_Roundworm.counts.tsv


title: H1W1_85vs15_pRNA_repl1

description:
Mix of GM12878.DF1 cell line and C.elegans strains mix (N2:Hawaii) RNA, 85:15 proportion, library preparation replicate 1
LOVSON_E1.Human_Roundworm.counts.tsv

value: clonal pro-B cell line GM12878.DF1 / N2 and Hawaii strains


title: H1W1_65vs35_pRNA_repl3

description:
Mix of GM12878.DF1 cell line and C.elegans strains mix (N2:Hawaii) RNA, 65:35 proportion, library preparation replicate 3
LOVSON_E1.Human_Roundworm.counts.tsv


title: hTERT-RPE1 Replicate 2, BrdU-IP Late

description:
hg19
haplotype-resolved
02_RPE1_WT_rep2_a_IP_Aneu_rmdup_w400ks400k_Percent_q0.05.bedGraph
02_RPE1_WT_rep2_b_IP_Aneu_rmdup_w400ks400k_Percent_q0.05.bedGraph

library_source: genomic

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 and a constructed B6/JF1 specific diploid genome (Sakata et al., 2017) for non-haplotype and haplotype-resolved analysis, respectively.
Genome coordinates of allele-specific uniquely mapped reads (MAPQ >16) were converted to mm9 by liftOver tool (UCSC Genome Browser). Duplicated reads were filtered out.
Reads per million (rpm) normalization were calculated for early- and late-S-phase BrdU-IP samples in sliding windows of 200-kb at 80-kb intervals and a nonoverlapping 400-kb bins for non-haplotype and haplotype-resolved analysis, respectively.
Then the ratio of early-S-phase to total read counts [(early-S reads)/(early-S reads + late-S reads)] was calculated for each bin, and their distribution was converted to fit within a ±1 scale. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Assembly: mm9
Supplementary files format and content: bedGraph
Library strategy: BrdU-IP Repli-seq

molecule: genomic DNA

source_name: retinal pigment epithelial cells

extract_protocol:
We followed the BrdU-IP-based protocol as described (Ryba et al., 2011). 75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early- and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 cell sorter (ultra-purity mode). Extracted DNA was sonicated by a Bioruptor UCD-250 (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

value: retinal pigment epithelial cells

value: Epithelial cells immortalized with hTERT


title: SARS-Cov-2 patient with with persistent olfactory symptoms (Group 1, P12)

description: miRNA expression profiling of patient with persistent olfactory symptoms  (Group 1, P12)


title: WT JB4/EI7HZ2 mESCs Replicate 3, RNA-seq


title: M1W1_27vs73_pRNA_repl2

description:
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 27:73 proportion, library preparation replicate 2
LOVSON_E1.Mouse_Roundworm.counts.tsv


title: SARS-Cov-2 patient with persistent olfactory symptoms  (Group 1, P11)

description: miRNA expression profiling of patient with persistent olfactory symptoms  (Group 1, P11)


title: hTERT-RPE1 Replicate 2, BrdU-IP Early


title: H1W1_65vs35_pRNA_repl2

description:
Mix of GM12878.DF1 cell line and C.elegans strains mix (N2:Hawaii) RNA, 65:35 proportion, library preparation replicate 2
LOVSON_E1.Human_Roundworm.counts.tsv


title: WT JB4/EI7HZ2 mESCs Replicate 2, RNA-seq


title: M1W1_27vs73_pRNA_repl1

description:
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 27:73 proportion, library preparation replicate 1
LOVSON_E1.Mouse_Roundworm.counts.tsv


title: hTERT-RPE1 Replicate 1, BrdU-IP Late

description:
hg19
haplotype-resolved
01_RPE1_WT_rep1_a_IP_Aneu_rmdup_w400ks400k_Percent_q0.05.bedGraph
01_RPE1_WT_rep1_b_IP_Aneu_rmdup_w400ks400k_Percent_q0.05.bedGraph


title: H1W1_65vs35_pRNA_repl1

description:
Mix of GM12878.DF1 cell line and C.elegans strains mix (N2:Hawaii) RNA, 65:35 proportion, library preparation replicate 1
LOVSON_E1.Human_Roundworm.counts.tsv


title: WT JB4/EI7HZ2 mESCs Replicate 1, RNA-seq


title: H1W1_85vs15_pRNA_repl2

description:
Mix of GM12878.DF1 cell line and C.elegans strains mix (N2:Hawaii) RNA, 85:15 proportion, library preparation replicate 2
LOVSON_E1.Human_Roundworm.counts.tsv


title: mouse1_spleen_chunk1_repl2_spikeinW2

description:
Mouse no.1 (129S1xCAST F1), spleen, with C.elegans (2:1 N2:Hawaii) RNA spike-in, library preparation replicate 2
POLMOT_E2.Mouse_Roundworm.counts.tsv


title: hTERT-RPE1 Replicate 1, BrdU-IP Early


title: SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 2, RNA-seq


title: SARS-Cov-2 patient with persistent olfactory symptoms  (Group 1, P14)

description: miRNA expression profiling of patient with persistent olfactory symptoms  (Group 1, P14)


title: CPG (.1uM), IFNAR;RelB-DBDB, 8h

status: Public on Jul 10 2023

city: Los Angeles

first: Hector

middle: I

last: Navarro

state: California

address: 570 Boyer Hall

department: MIMG

institute: UCLA

data_processing:
Reads were trimmed using cutadapt (1) (cutoff q=20) and mapped to the mm10 genome.
The October 2014 version of the Ensembl database was used to extract gene annotation information.
CPM values were generated using edgeR (5) to normalize the raw counts data based on sequencing depth
Assembly: mm10
Supplementary files format and content: .xlsx

source_name: Bone Marrow

growth_protocol: Bone marrow cells were isolated from mouse femurs and cultured with 20 ng/ml GM-CSF and 10 ng/ml IL-4 to produce BMDCs with half the media being replaced on day 3 and 6 as previously reported

extract_protocol:
Collected in Invitrogen™ TRIzol™ Reagent (Cat# 15-596-018) for RNA and was extracted using Qiagen RNeasy Mini Kit
RNA was used for Illumina bead Arrays as described (Cheng et al 2017) and for RNA-seq as described (Sen et al 2020). Briefly, libraries were prepped using KAPA Stranded mRNA-Seq Kit Illumina® platform KR0960 – v3.15 using 1µg of RNA per sample measured using Qubit 2.0 fluorometer. Final libraries were checked via agarose gel and multiplexed with a maximum of 24 samples per sequencing reaction. Libraries were sequenced using Illumina HiSeq 3000 with single end 50bp reads

treatment_protocol: Cells were stimulated with CpG (0.1µM) (Invivogen ODN 1668 Cat# tlrl-1668) and collected at specified timepoints

value: Bone Marrow

value: BMDCs

value: IFNAR;RelB-DBDB

value: CPG (.1uM)

tag: time


title: CPG (.1uM), IFNAR;RelB-DBDB, 3h

value: IFNAR;RelB--DBDB


title: Control, IFNAR;RelB-DBDB, 1h

value: Control


title: CPG (.1uM), RelB-DBDB, 1h

value: RelB-DBDB


title: CPG (.1uM), RelB-DBDB, 3h


title: mouse1_spleen_chunk1_repl1_spikeinW1

description:
Mouse no.1 (129S1xCAST F1), spleen, with C.elegans (1:1 N2:Hawaii) RNA spike-in, library preparation replicate 1
POLMOT_E2.Mouse_Roundworm.counts.tsv

value: spleen / whole organism

value: 129S1/SvImJ x Cast/EiJ F1 / N2 x Hawaii


title: RelBko_BMDCs_1.0h_RelB_ChIP, LPS (10ng/mL)

description:
rpkms_ann.txt
S5_RelBKO_1.0h_RelB_sorted.bam_RPKM
S5_RelBKO_1.0h_RelB_sorted

data_processing:
Reads were aligned using Hisat2 to the mouse genome (NCBI37/mm9).
Peaks were called if they were enriched compared to input samples and had a false discovery rate of < 0.01 using HOMER software (Heinz et al., 2010).
To compare peaks across samples, a master probe which contained all peaks from every sample was generated using BEDTools (Quinlan et al., 2010).
Then SeqMonk was used to find raw read counts for each peak in the master probe.
RPKMs were generated using the length of each peak and the depth of sequencing for each sample.
Assembly: mm9
Supplementary files format and content: .tdf and RPKM

extract_protocol:
ChIP-seq was performed as previously described (Barish et al., 2010; Lee et al., 2006) with anti-RelA antibody (Cell Signaling, 8242). Approximately 10 million BMDCs were used per sample. Two chemical crosslinkers, DSG and PFA, were used during sample preparation at concentrations of 1.0mM and 1.0%, respectively. Sonication was performed on a Covaris M220 focused ultrasonicator.
ChIP-seq libraries were prepared using KAPA HyperPrep Kits (Roche).

treatment_protocol: Cells were stimulated with LPS stimulation (10ng/mL)  (Invivogen ODN 1668 Cat# tlrl-1668) and collected at specified timepoints

tag: antibody

value: anti-RelB antibody (Cell Signaling D7D7W or #10544)

value: RelBko

value: LPS (10ng/mL)


title: Input Sample

description:
rpkms_ann.txt
Sinput_S7_R1_001_sorted.bam_RPKM
Sinput_S7_R1_001_sorted

value: WT


title: RelBko_BMDCs_1.0h_RelA_ChIP, LPS (10ng/mL)

description:
rpkms_ann.txt
S6_RelBKO_1.0h_RelA_sorted.bam_RPKM
S6_RelBKO_1.0h_RelA_sorted

value: anti-RelA antibody (Cell Signaling, 8242)


title: CPG (.1uM), IFNAR;RelB-DBDB, 1h


title: WT_BMDCs_1.0h_RelA_ChIP, LPS (10ng/mL)

description:
rpkms_ann.txt
S3_WT_1.0h_RelA_sorted.bam_RPKM
S3_WT_1.0h_RelA_sorted

value: anti-RelA antibody (Cell Signaling, D14E12or #8242)


title: WT_BMDCs_1.0h_RelB_ChIP, LPS (10ng/mL)

description:
rpkms_ann.txt
S2_WT_1.0h_RelB_sorted.bam_RPKM
S2_WT_1.0h_RelB_sorted


title: WT_BMDCs_0.0h_RelB_ChIP

description:
rpkms_ann.txt
S1_WT_0.0h_RelB_sorted.bam_RPKM
S1_WT_0.0h_RelB_sorted


title: Control, RelB-DBDB, 1h


title: SARS-Cov-2 patient with persistent olfactory symptoms  (Group 1, P21)

description: miRNA expression profiling of patient with persistent olfactory symptoms  (Group 1, P21)

value: olfactory epithelium


title: mid9_07_D05

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TUD

data_processing:
basecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
preparation of reference:  Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
mapping:  Reads were aligned to the axolotl reference genome AmexG_v6.0-DD using the aligner STAR (v2.7.6a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
counts per feature:  Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters:  -a AmexG_v6_DD.gtf -s 0 -p -o bfx1267.AmexG_v6_DD.tsv -Q 1).
Assembly: AmexG_v6.0-DD
Supplementary files format and content: bfx1267.AmexG_v6_DD.tsv.gz is a tab-separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts and additional gene information. Column titles

organism: Ambystoma mexicanum

source_name: Blastema

extract_protocol:
Blastemas samples were collected from mid- (13 dpa), late (15 dpa)- or palette-stage (18 dpa) animals at 48 h following GalNP(Rho) injection. Samples were dissociated in 400 ml of 1x Liberase (Roche) diluted in 0.8x PBS, using mechanical disruption with forceps together with smooth pipetting at room temperature for 30 min. For live/dead staining, suspensions were incubated in 0.8X PBS supplemented with 200 nM CellTrace calcein green AM (Invitrogen) and 12.5 uM SYTOX blue (Invitrogen) at room temperature for 15 min. Subsequently, cell suspensions were filtered through a 70-mm-diameter strainer to generate single-cell suspensions and immediately subjected to FACS. Alive cells were sorted using a FACSAria III equipped with a 100 mm nozzle (BD Biosciences) according to the presence or absence of rhodamine signal using blastemas from vehicle-injected axolotls as negative controls. Single rhodamine+ cells were sorted into 2 μl of lysis buffer (nuclease-free water, 0.2% Triton X100, 4U/μl RNase Inhibitor).
Processing of the samples for RNA-sequencing was done following a modified Smartseq-2 protocol (https://star-protocols.cell.com/protocols/1595). In brief, samples were thawed on ice and we added 0.5ul of dT-buffer to each sample, containing poly-dT oligos (final concentration of 0.5uM) for capturing mRNAs. Subsequently, we performed reverse transcription and cDNA amplification. Libraries were prepared with the Illumina® DNA Prep Tagmentation kit and sequenced on an Illumina NovaSeq 6000 S1 flow cell to an average of 0.85 mio PE50bp fragments/cell.

treatment_protocol: Axolotls were amputated through the upper limb, and injected with GalNP-rho at 48 hr prior to blastema collection

value: d/d

value: Blastema

tag: regeneration stage

value: Mid


title: mid9_07_D04


title: mid9_07_D03


title: mid9_07_D06


title: mid9_07_D01


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title: mid9_07_D07


title: mid9_07_D02


title: mid9_07_C22


title: mid9_07_C23


title: mid9_07_C24


title: RelBko_BMDCs_0.0h_RelB_ChIP,

description:
rpkms_ann.txt
S4_RelBKO_0.0h_RelB_sorted.bam_RPKM
S4_RelBKO_0.0h_RelB_sorted

value: Bone Marrow

value: BMDCs


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title: CPG (.1uM), RelB-DBDB, 8h

value: CPG (.1uM)


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title: pal7_02_F04


title: pal7_02_F06


title: pal7_02_F22


title: pal7_02_F16


title: pal7_02_F14


title: pal7_02_F05


title: pal7_02_F11


title: pal7_02_F12


title: pal7_02_E21


title: pal7_02_F13


title: pal7_02_F09


title: pal7_02_F03


title: pal7_02_F07


title: pal7_02_F08


title: pal7_02_F02


title: pal7_02_E24


title: pal7_02_E19


title: pal7_02_F01


title: pal7_02_E14


title: pal7_02_E20


title: pal7_02_E17


title: pal7_02_E16


title: pal7_02_E22


title: pal7_02_E18


title: pal7_02_E13


title: pal7_02_E15


title: pal7_02_E11


title: pal7_02_E12


title: pal7_02_E06


title: pal7_02_E10


title: pal7_02_E04


title: pal7_02_E09


title: pal7_02_E05


title: pal7_02_E08


title: pal7_02_E03


title: pal7_02_E07


title: pal7_02_E23


title: pal7_02_E02


title: pal6_02_D22


title: pal6_02_D24


title: pal7_02_D18


title: pal6_02_D20


title: pal7_02_E01


title: pal6_02_D23


title: pal6_02_D21


title: pal7_02_D19


title: pal7_02_D15


title: pal7_02_D16


title: pal7_02_D11


title: pal7_02_D12


title: pal7_02_D17


title: pal7_02_D13


title: pal7_02_D10


title: pal7_02_D14


title: pal7_02_D08


title: pal7_02_D09


title: pal7_02_D05


title: pal7_02_D04


title: pal7_02_D06


title: pal7_02_D07


title: pal7_02_D03


title: pal7_02_D02


title: pal6_02_C22


title: pal6_02_C24


title: pal6_02_C23


title: pal6_02_C14


title: pal6_02_C15


title: pal6_02_C19


title: pal6_02_C11


title: pal6_02_C18


title: pal6_02_C17


title: pal6_02_C21


title: pal6_02_C12


title: pal6_02_C20


title: pal6_02_C10


title: pal7_02_D01


title: pal6_02_C08


title: pal6_02_C09


title: pal6_02_C03


title: pal6_02_C16


title: pal6_02_C01


title: pal6_02_B23


title: pal6_02_C05


title: pal6_02_C07


title: pal6_02_B22


title: pal6_02_C02


title: pal6_02_B24


title: pal6_02_B17


title: pal6_02_B20


title: pal6_02_B19


title: pal6_02_B18


title: pal6_02_B16


title: pal6_02_B14


title: pal6_02_B15


title: pal6_02_C04


title: pal6_02_B13


title: pal6_02_B09


title: pal6_02_B11


title: pal6_02_B10


title: pal6_02_C06


title: pal6_02_B12


title: pal6_02_B08


title: pal6_02_B05


title: pal6_02_B04


title: pal6_02_B03


title: pal6_02_B21


title: pal6_02_B02


title: pal6_02_B01


title: pal6_02_A24


title: pal6_02_A23


title: pal6_02_A21


title: pal6_02_A22


title: pal6_02_A13


title: pal6_02_B07


title: pal6_02_A14


title: pal6_02_A17


title: pal6_02_A18


title: pal6_02_A19


title: pal6_02_A09


title: pal6_02_A06


title: pal6_02_A20


title: pal6_02_B06


title: pal6_02_A16


title: pal6_02_A11


title: pal6_02_A15


title: pal6_02_A10


title: pal6_02_A03


title: pal5_01_P22


title: pal5_01_P21


title: pal5_01_P18


title: pal5_01_P19


title: pal6_02_A05


title: pal6_02_A08


title: pal6_02_A07


title: pal6_02_A01


title: pal5_01_P24


title: pal6_02_A02


title: pal5_01_P23


title: pal5_01_P13


title: pal5_01_P16


title: pal5_01_P20


title: pal5_01_P10


title: pal5_01_P12


title: pal5_01_P08


title: pal5_01_P07


title: pal6_02_A12


title: pal6_02_A04


title: pal5_01_P15


title: pal5_01_P14


title: pal5_01_P11


title: pal5_01_P09


title: pal5_01_P05


title: pal5_01_P06


title: pal5_01_O19


title: pal5_01_O22


title: pal5_01_O15


title: pal5_01_O08


title: pal5_01_O14


title: pal5_01_O12


title: pal5_01_P04


title: pal5_01_O17


title: pal5_01_O04


title: pal5_01_P03


title: pal5_01_P02


title: pal5_01_O10


title: pal5_01_O01


title: pal5_01_P01


title: pal5_01_P17


title: pal5_01_O24


title: pal5_01_O23


title: pal5_01_N23


title: pal5_01_O21


title: pal5_01_O20


title: pal5_01_N21


title: pal5_01_N16


title: pal5_01_O18


title: pal5_01_N15


title: pal5_01_N14


title: pal5_01_O16


title: pal5_01_O13


title: pal5_01_N12


title: pal5_01_N11


title: pal5_01_O07


title: pal5_01_O06


title: pal5_01_N09


title: pal5_01_O05


title: pal5_01_O03


title: pal5_01_O02


title: pal5_01_O11


title: pal5_01_O09


title: pal5_01_N05


title: pal5_01_N07


title: pal5_01_N04


title: pal5_01_N03


title: pal5_01_N24


title: pal5_01_N13


title: pal5_01_N22


title: pal5_01_M23


title: pal5_01_N20


title: pal5_01_M21


title: pal5_01_N19


title: pal5_01_N17


title: pal5_01_N18


title: pal5_01_M18


title: pal5_01_N02


title: pal5_01_N10


title: pal5_01_M10


title: pal5_01_M08


title: pal5_01_M07


title: pal5_01_M04


title: pal5_01_N08


title: pal5_01_M01


title: pal5_01_M14


title: pal5_01_L24


title: pal5_01_L22


title: pal5_01_N06


title: pal5_01_M09


title: pal5_01_M06


title: pal5_01_M24


title: pal5_01_N01


title: pal5_01_M22


title: pal5_01_L20


title: pal5_01_L19


title: pal5_01_L17


title: pal5_01_M20


title: pal5_01_M19


title: pal5_01_L13


title: pal5_01_L16


title: pal5_01_L15


title: pal5_01_L12


title: pal5_01_L10


title: pal5_01_M17


title: pal5_01_M15


title: pal5_01_L11


title: pal5_01_M16


title: pal5_01_M12


title: pal5_01_M11


title: pal5_01_M13


title: pal5_01_M05


title: pal5_01_M03


title: pal5_01_L04


title: pal5_01_M02


title: pal5_01_L23


title: pal5_01_K21


title: pal5_01_L21


title: pal5_01_K17


title: pal5_01_K19


title: pal5_01_L18


title: pal5_01_L05


title: pal5_01_L09


title: pal4_01_K13


title: pal5_01_L08


title: pal5_01_K23


title: pal5_01_K09


title: pal5_01_K05


title: pal5_01_L07


title: pal5_01_K18


title: pal5_01_L03


title: pal5_01_L14


title: pal5_01_L02


title: pal5_01_K03


title: pal5_01_K02


title: pal4_01_J24


title: pal4_01_J23


title: pal4_01_J21


title: pal5_01_L01


title: pal4_01_J20


title: pal5_01_K24


title: pal4_01_K14


title: pal4_01_K16


title: pal4_01_J17


title: BCX-094 biol repl 3

city: Houston

first: Khandan

last: Keyomarsi

state: Texas

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: University of Texas - MD Anderson Cancer Center

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the combined reference genome (Gencode human GRCh38 and mouse GRCm38 concatenated) using TopHat2 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 1.6.3) in order to generate read count data on gene/feature level (parameters: -p -t exon -g gene_id -s 0)
Genes/features were annotated using the combined GTF file from Gencode human GRCh38 and mouse GRCm38 references
Only the reads that were mapped to the human genome were kept, whereas the reads mapped to the mouse genome were removed
Assembly: Human GRCh38 and mouse GRCm38
Supplementary files format and content: Raw read count data generated by featureCounts (Subread 1.6.3) for each sample

source_name: patient-derived xenograft

extract_protocol:
Total RNA was isolated from cell lysates using Trizol reagent (Ambion Life Technologies) according to manufacturer's protocol
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc (US) following standard Illumina protocols

value: patient-derived xenograft

tag: disease state

value: metastatic breast cancer

value: TNBC-IM


title: pal5_01_L06


title: pal4_01_J16


title: pal4_01_J15


title: BCX-094 biol repl 1


title: pal5_01_K12


title: pal5_01_K11


title: BCX-094 biol repl 4


title: pal4_01_J14


title: pal5_01_K22


title: pal5_01_K20


title: pal5_01_K10


title: pal4_01_J13


title: PR-4 biol repl 6

value: Palbociclib resistant


title: pal5_01_K08


title: PR-4 biol repl 4


title: pal4_01_J12


title: pal5_01_K07


title: pal5_01_K06


title: PR-4 biol repl 3


title: BCX-094 biol repl 2


title: pal4_01_K15


title: pal5_01_K04


title: pal4_01_J10


title: pal5_01_K01


title: pal4_01_J22


title: PR-4 biol repl 1


title: pal4_01_J09


title: pal4_01_J19


title: PR-3 biol repl 6


title: pal4_01_J18


title: PR-4 biol repl 5


title: pal4_01_J05


title: pal4_01_J07


title: PR-3 biol repl 2


title: PR-3 biol repl 1


title: PR-4 biol repl 2


title: PR-2 biol repl 6


title: pal4_01_J08


title: pal4_01_J06


title: PR-3 biol repl 4


title: PR-3 biol repl 3


title: PR-2 biol repl 4


title: pal4_01_I22


title: pal4_01_I24


title: pal4_01_J04


title: PR-2 biol repl 5


title: pal4_01_I20


title: pal4_01_J02


title: pal4_01_I21


title: PR-3 biol repl 5


title: PR-1 biol repl 6


title: PR-1 biol repl 5


title: pal4_01_J03


title: pal4_01_J11


title: pal4_01_I18


title: PR-1 biol repl 4


title: pal4_01_I23


title: PR-2 biol repl 3


title: PR-1 biol repl 2


title: PR-2 biol repl 2


title: PR-1 biol repl 3


title: PR-2 biol repl 1


title: pal4_01_I14


title: pal4_01_I19


title: pal4_01_I13


title: ET-R biol repl 11

value: Endocrine therapy resistant and CDK4/6i sensitive


title: pal4_01_I17


title: pal4_01_I09


title: pal4_01_I11


title: pal4_01_J01


title: pal4_01_I16


title: PR-1 biol repl 1


title: pal4_01_I15


title: pal4_01_I07


title: ET-R biol repl 12


title: ET-R biol repl 13


title: pal4_01_I12


title: ET-R biol repl 3


title: pal4_01_I10


title: ET-R biol repl 1


title: ET-R biol repl 9


title: pal4_01_I08


title: ET-R biol repl 6


title: pal4_01_H23


title: pal4_01_H24


title: pal4_01_I06


title: ET-R biol repl 4


title: ET-R biol repl 5


title: pal4_01_H22


title: pal4_01_I04


title: pal4_01_I05


title: pal4_01_H21


title: pal4_01_I03


title: PR-3 biol rep 6

source_name: Organoids

value: Organoids

value: Breast Cancer Organoids

value: Palbociclib-resistant


title: PR-3 biol rep 5


title: pal4_01_I02


title: ET-R biol repl 2


title: pal4_01_I01


title: PR-3 biol rep 7


title: pal4_01_H19


title: pal4_01_H20


title: ET-R biol repl 10


title: pal4_01_H18


title: PR-3 biol rep 1


title: pal4_01_H17


title: PR-2 biol rep 4


title: ET-R biol repl 8


title: ET-R biol repl 7


title: PR-3 biol rep 4


title: PR-2 biol rep 2


title: PR-3 biol rep 3


title: PR-3 biol rep 2


title: pal3_01_H12


title: pal4_01_H15


title: pal3_01_H11


title: ET-R biol rep 3


title: PR-2 biol rep 3


title: PR-2 biol rep 1


title: PR-1 biol rep 1


title: pal3_01_H07


title: pal3_01_H09


title: PR-1 biol rep 2


title: pal4_01_H16


title: pal3_01_H05


title: pal3_01_H10


title: pal3_01_H06


title: pal3_01_H08


title: ET-R biol rep 4


title: ET-R biol rep 2


title: pal3_01_H02


title: pal3_01_H04


title: ET-R biol rep 1


title: pal3_01_H03


title: pal4_01_G24


title: T47D 3.6 Palbo-resistant  biol rep 2

data_processing:
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the human reference genome (Gencode GRCh38) using TopHat 2.1.1 (parameter: --library-type=fr-unstranded)
The BAM file with mapped reads for each sample was sorted and then used as an input for HTSeq 0.11.0 in order to generate read count data on gene/feature level (parameters: -s no  -m union)
Assembly: GRCh38
Supplementary files format and content: raw read count data generated by htseq-count 0.11.0 for each sample

growth_protocol: Cells were maintained in minimum essential medium Eagle alpha modification (alpha MEM) supplemented with 10% FBS, 10mM HEPES, nonessential amino acids, sodium pyruvate, 2mM L-glutamine, insulin, EGF, and hydrocortisone

treatment_protocol:
Palbociclib-resistant cell lines were generated by culturing cells in media supplemented with palbociclib at increasing concentrations for 6 months starting at 1.2 uM and reaching a final dose of 4.8uM. Abemaciclib-resistant cells were generated by culturing cells in media supplemented with abemaciclib at increasing concentrations for 7 months starting at 0.5 uM and reaching a final dose of 1.5 uM
Resistant cells were maintained in alpha MEM supplemented with palbociclib or abemaciclib at the same concentration that cells were resistant, but all experiments were conducted in the absence of drug-supplemented media unless otherwise noted.

value: Breast Cancer Cells

value: 3.6 uM Palbociclib-resistant


title: T47D 3.6 Palbo-resistant  biol rep 3


title: T47D 3.6 Palbo-resistant  biol rep 1


title: T47D 4.8 Palbo-resistant  biol rep 3

value: 4.8 uM Palbociclib-resistant


title: T47D 2.4 Palbo-resistant  biol rep 3

value: 2.4 uM Palbociclib-resistant


title: T47D 4.8 Palbo-resistant  biol rep 2


title: T47D 2.4 Palbo-resistant  biol rep 2


title: T47D 4.8 Palbo-resistant  biol rep 1


title: pal3_01_H01

value: d/d

value: Blastema


title: pal4_01_G23


title: pal4_01_G19


title: pal4_01_G16


title: pal4_01_G17


title: pal4_01_G20


title: T47D 1.2 Palbo-resistant  biol rep 1

value: 1.2 uM Palbociclib-resistant


title: T47D 2.4 Palbo-resistant  biol rep 1


title: T47D 1.2 Palbo-resistant  biol rep 2


title: T47D 1.2 Palbo-resistant  biol rep 3


title: pal4_01_G18


title: pal4_01_G21


title: T47D Parental biol rep 2

value: CDK4/6i sensitive


title: pal3_01_G09

value: Palette


title: MCF7 1.0 Abema-resistant  biol rep 2

value: 1.0 uM Abemaciclib-resistant


title: T47D Parental biol rep 3


title: T47D Parental biol rep 1


title: MCF7 1.5 Abema-resistant  biol rep 1

value: 1.5 uM Abemaciclib-resistant


title: pal3_01_G11


title: pal3_01_G08


title: pal3_01_G07


title: pal4_01_G15


title: MCF7 1.0 Abema-resistant  biol rep 1


title: pal3_01_G10


title: MCF7 1.5 Abema-resistant  biol rep 3


title: MCF7 0.5 Abema-resistant  biol rep 2

value: 0.5 uM Abemaciclib-resistant


title: pal4_01_G22


title: pal3_01_G12


title: pal3_01_G05


title: MCF7 1.0 Abema-resistant  biol rep 3


title: MCF7 1.5 Abema-resistant  biol rep 2


title: MCF7 0.5 Abema-resistant  biol rep 1


title: pal3_01_G06


title: MCF7 Parental biol rep 5


title: MCF7 Parental biol rep 4


title: pal3_01_G03


title: pal3_01_G04


title: MCF7 Parental biol rep 6


title: pal3_01_G02


title: pal3_01_G01


title: MCF7 4.8 Palbo-resistant  biol rep 1


title: MCF7 3.6 Palbo-resistant  biol rep 3


title: pal3_01_F22


title: pal3_01_F23


title: MCF7 0.5 Abema-resistant  biol rep 3


title: MCF7 4.8 Palbo-resistant  biol rep 3


title: MCF7 3.6 Palbo-resistant  biol rep 1


title: pal3_01_F20


title: MCF7 2.4 Palbo-resistant  biol rep 3


title: MCF7 4.8 Palbo-resistant  biol rep 2


title: pal3_01_F18


title: pal3_01_F17


title: pal3_01_F21


title: MCF7 3.6 Palbo-resistant  biol rep 2


title: MCF7 2.4 Palbo-resistant  biol rep 2


title: pal3_01_F19


title: MCF7 2.4 Palbo-resistant  biol rep 1


title: MCF7 1.2 Palbo-resistant  biol rep 2


title: MCF7 1.2 Palbo-resistant  biol rep 1


title: pal3_01_F16


title: pal3_01_F15


title: pal3_01_F13


title: MCF7 Parental biol rep 3


title: pal3_01_F24


title: pal3_01_F12


title: MCF7 Parental biol rep 2


title: MCF7 Parental biol rep 1


title: pal3_01_F11


title: pal3_01_F10


title: pal3_01_F09


title: MCF7 1.2 Palbo-resistant  biol rep 3


title: IP library of the region of 75kDa-150kDa on the membrane of v5 only samples

city: La Jolla

first: Gene

middle: W

last: Yeo

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
Reads were adapter-trimmed using Cutadapt (v1.14) and mapped to human-specific repetitive elements from RepBase (version 18.05) by STAR (v2.4.0i)(Dobin et al., 2013).
Repeat-mapping reads were removed, and remaining reads were mapped to the human genome assembly (hg19) with STAR
Repeat-mapping reads were removed, and remaining reads were mapped to the human genome assembly (hg19) with STAR. PCR duplicate reads were removed using the unique molecular identifier (UMI) sequences in the 5’ adapter and remaining reads retained as ‘usable reads’.
Peaks were called on the usable reads by CLIPper (Lovci et al., 2013) and assigned to gene regions annotated in GENCODE (hg19) with the following descending priority order: CDS, 5’UTR, 3’UTR, proximal intron, and distal intron. Proximal intron regions are defined as extending up to 500 bp from an exon-intron junction. Each peak was normalized to the size-matched input (SMInput) by calculating the fraction of the number of usable reads from immunoprecipitation to that of the usable reads from the SMInput. Peaks were deemed significant at 8-fold enrichment and p-value10-3(Chi-squared test, or Fisher’s exact test if the observed or expected read number in eCLIP or SMInput was below 5).
Assembly: hg19
Supplementary files format and content: bigwig files for input and IP samples as well as beds files for significant eCLIP peaks per experimental group

growth_protocol: Stable lines were made in human lenti-X HEK293T cells (HEK293XT, Takara Bio), maintained in DMEM (4.5 g l−1 D-glucose) supplemented with 10% FBS (Gibco) at 37 °C with 5% CO2. Cells were passaged at 70-90% confluency by rinsing cells gently with DPBS without calcium and magnesium (Corning) then dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10.

extract_protocol:
All eCLIPs were conducted following induction or transient transfections and IP was conducted using anti-V5 tag (Bethyl A190-120A) and V5-tag or His-tag (both from Proteintech). eCLIP experiments were performed as previously described in a detailed standard operating procedure6 (6. Van Nostrand, E. L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016). ) In brief, 20 million cross-linked cells were lysed and sonicated, followed by treatment with RNase I (Thermo Fisher) to fragment RNA. Antibodies were precoupled to species-specific (anti-rabbit IgG) dynabeads (Thermo Fisher), added to lysate and incubated overnight at 4 °C. Before IP washes, 2% of sample was removed to serve as the paired-input sample. For IP samples, high-salt and low-salt washes were performed, after which RNA was dephosphorylated with FastAP (Thermo Fisher) and T4 PNK (NEB) at low pH, and a 3′ RNA adapter was ligated with T4 RNA ligase (NEB). Ten percent of IP and input samples were run on an analytical PAGE Bis-Tris protein gel, transferred to PVDF membrane, blocked in 5% dry milk in TBST, incubated with the same primary antibody used for IP (typically at 1:4,000 dilution), washed, incubated with secondary horseradish peroxidase-conjugated species-specific TrueBlot antibody (Rockland) and visualized with standard enhanced chemiluminescence imaging to validate successful IP. Ninety percent of IP and input samples were run on an analytical PAGE Bis-Tris protein gel and transferred to nitrocellulose membranes, after which the region from the protein size to 75 kDa above protein size was excised from the membrane, treated with proteinase K (NEB) to release RNA and concentrated by column purification (Zymo).
RNA was isolated from the membrane, reverse transcribed with AffinityScript (Agilent), free primers were removed (ExoSap-IT, Affymetrix), and a 5’ DNA adapter was ligated onto the cDNA product with T4 RNA ligase (NEB). Libraries were then amplified with Q5 PCR mix (NEB), size selected using AMPure XP beads (Beckman Coulter, Inc.) and on a 3% agarose gel, and then quantified with a Bioanalyzer instrument (Agilent). Paired-end (50 base pair) sequencing of the eCLIP libraries were performed on Illumina HiSeq 3500.
enhanced CLIP

treatment_protocol:
No treatments were added
No treatments were added

value: Human embryonic kidney


title: IP library of the region of 100kDa-225kDa on the membrane of v5 only samples


title: IP library of the region of 25kDa-100kDa on the membrane of v5 only samples


title: pal3_01_F08


title: pal3_01_F07


title: pal3_01_F05


title: pal3_01_F06


title: pcDNA6 IP

value: pcDNA6/myc-His B


title: IP library of the region of 50kDa-125kDa on the membrane of v5 only samples


title: pcDNA6 INPUT


title: V5-pDEST_INPUT


title: pal3_01_F14


title: V5-pDEST_IP


title: YWHAZ_rep2_IP

value: YWHAZ-V5 overexpressed


title: pal3_01_F02


title: pal3_01_E24


title: YWHAZ_rep1_IP


title: pal3_01_E23


title: YWHAZ_rep1_INPUT


title: pal3_01_E21


title: pal3_01_F03


title: pal3_01_F04


title: pal3_01_E22


title: YWHAE_rep2_INPUT

value: YWHAE-V5 overexpressed


title: YWHAE_rep1_INPUT


title: YWHAE_rep1_IP


title: pal3_01_E19


title: pal3_01_E18


title: pal3_01_E20


title: pal3_01_F01


title: pal3_01_E14


title: YWHAH_rep2_INPUT

value: YWHAH-V5 overexpressed


title: YWHAH_rep1_INPUT


title: pal3_01_E17


title: YWHAZ_rep2_INPUT


title: YWHAH_rep1_IP


title: pal3_01_E16


title: pal3_01_E12


title: pal3_01_E13


title: YWHAG_rep2_IP

value: YWHAG-V5 overexpressed


title: pal3_01_E11


title: YWHAG_rep2_INPUT


title: YWHAG_rep1_IP


title: YWHAG_rep1_INPUT


title: YWHAE_rep2_IP


title: pal3_01_E10


title: pal3_01_E09


title: HSP90A_rep2_INPUT

value: HSP90A-V5 overexpressed


title: HSP90A_rep2_IP


title: YWHAH_rep2_IP


title: HSP90A_rep1_IP


title: pal3_01_E15


title: pal3_01_E07


title: pal3_01_E05


title: NR5A1_DD_rep2_IP


title: pal3_01_E06


title: NR5A1_DD_rep2_INPUT


title: NR5A1_DD_rep1_INPUT


title: NR5A1_rep1_INPUT

value: NR5A1-V5 overexpressed


title: NR5A1_rep2_INPUT


title: NR5A1_rep2_IP


title: NR5A1_DD_rep1_IP


title: NR5A1_rep1_IP


title: leaf 5, ZmPep3 2h, rep6

city: Bern

first: Matthias

last: Erb

address: Altenbergrain 21

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

data_processing:
BGISEQ
Sequencing reads were filtered for adaptors, reads with more than 5% unknown bases (N) and low quality reads with the software SOAPnuke.
Filtered reads were mapped to GCF_000005005.2_B73_RefGen_v4 using Bowtie2.
Reads count and gene expression level were deteremined by RSEM.
Assembly: GCF_000005005.2_B73_RefGen_v4
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FRKM counts for each sample

organism: Zea mays

source_name: leaf

growth_protocol: Maize (Zea mays, line B73) seeds were sown directly into pots (9 cm x 9 cm x 10 cm) with commercial soil (Selmaterra, BiglerSamen, Switzerland). All plants were grown in a glasshouse supplemented with artificial lights (~300 μmol m-2 s-1) at 22 ± 2 °C, 40–60% relative humidity (RH), with a 14 h : 10 h, light : dark cycle.

extract_protocol:
Total RNA extraction was done with the GeneJET PCR Purification Kit (K0702, Thermo Scientific). DNAse I (M0303, New England BioLabs) treatment was done to minimize genomic DNA contamination. Total RNA sample quality control was done with the Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
Library construction was done by BGI following the DNBSEQ protocol.

treatment_protocol: V4 seedlings were cut at the position of 2nd leaf with a razor blade. L4, L5 and L6 leaves were carefully separated, all leaves were further cut by 0.5 cm under water. For L4 leaves (mature leaves), an additional removal of leaf sheath was required before further cutting of the leaf blade under water. All plant materials were transferred into glass beakers (250 mL) with 150 mL Milli-Q water and allowed for recovery for at least 2 hours before treatment. Detached leaves were transferred into 12-ml plastic centrifuge tubes containing 10 ml Milli-Q water. These samples were then transferred into the glass cylinders supplied with clean airflow for at least 2 hours acclimation. ZmPep3 treatment was done by adding 10 μl of a 1mM ZmPep3 solution in the centrifuge tubes to achieve a final concentration of around 1 µM. HAC treatment was done using the volatile dispensers. Whole leaf samples were harvested with 6 biological replicates for each leaf type/treatment/time combination by flash freezing in liquid nitrogen.

value: leaf

value: ZmPep3 2h


title: leaf 6, ZmPep3 2h, rep5


title: leaf 6, ZmPep3 2h, rep2


title: leaf 6, ZmPep3 2h, rep4


title: leaf 6, ZmPep3 2h, rep1


title: PIAS4_DD_rep2_IP


title: PIAS4_DD_rep1_INPUT


title: pal3_01_E08

value: d/d

value: Blastema


title: leaf 6, ZmPep3 2h, rep6


title: PIAS4_DD_rep2_INPUT


title: HSP90A_rep1_INPUT


title: pal3_01_E02


title: PIAS4_DD_rep1_IP


title: leaf 5, ZmPep3 2h, rep4


title: leaf 5, ZmPep3 2h, rep5


title: pal3_01_E03


title: leaf 6, ZmPep3 2h, rep3


title: PIAS4_rep2_INPUT

value: PIAS4-V5 overexpressed


title: pal3_01_E04

value: Palette


title: PIAS4_rep1_INPUT


title: pal3_01_E01


title: leaf 5, ZmPep3 2h, rep3


title: leaf 5, ZmPep3 2h, rep2


title: pal3_01_D24


title: pal3_01_D23


title: INO80B_DD_rep2_INPUT


title: PIAS4_rep1_IP


title: INO80B_DD_rep2_IP


title: PIAS4_rep2_IP


title: pal3_01_D22


title: pal3_01_D20


title: INO80B_rep2_INPUT

value: INO80B-V5 overexpressed


title: INO80B_DD_rep1_IP


title: MCCC1_DD_rep3_INPUT


title: INO80B_rep1_INPUT


title: leaf 4, ZmPep3 2h, rep6


title: INO80B_DD_rep1_INPUT


title: pal3_01_D21


title: INO80B_rep2_IP


title: pal3_01_D19


title: MCCC1_DD_rep3_IP


title: leaf 4, ZmPep3 2h, rep3


title: leaf 4, ZmPep3 2h, rep5


title: pal3_01_D18


title: leaf 5, ZmPep3 2h, rep1


title: MCCC1_DD_rep2_IP


title: leaf 4, ZmPep3 2h, rep2


title: pal3_01_D17


title: MCCC1_DD_rep1_INPUT


title: MCCC1_DD_rep1_IP


title: leaf 4, ZmPep3 2h, rep1


title: MCCC1_rep3_INPUT

value: MCCC1-V5 overexpressed


title: MCCC1_rep3_IP


title: MCCC1_DD_rep2_INPUT


title: leaf 4, ZmPep3 2h, rep4


title: leaf 6, HAC 2h, rep5

value: HAC 2h


title: INO80B_rep1_IP

value: Human embryonic kidney


title: pal3_01_D15


title: pal3_01_D14


title: pal3_01_D13


title: leaf 6, HAC 2h, rep3


title: leaf 6, HAC 2h, rep2


title: MCCC1_rep2_IP


title: ACTN3_DD_rep2_INPUT


title: MCCC1_rep1_INPUT


title: ACTN3_DD_rep3_INPUT


title: leaf 6, HAC 2h, rep6


title: ACTN3_DD_rep3_IP


title: MCCC1_rep1_IP


title: pal3_01_D12


title: ACTN3_DD_rep1_INPUT


title: ACTN3_DD_rep2_IP


title: pal2_01_D10


title: leaf 5, HAC 2h, rep6


title: leaf 6, HAC 2h, rep1


title: ACTN3_rep3_INPUT

value: ACTN3-V5 overexpressed


title: ACTN3_rep3_IP


title: ACTN3_rep2_INPUT


title: ACTN3_rep2_IP


title: ACTN3_rep1_INPUT


title: leaf 5, HAC 2h, rep5


title: pal3_01_D11


title: leaf 6, HAC 2h, rep4


title: pal2_01_D09


title: ACTN3_DD_rep1_IP


title: ACTN3_rep1_IP


title: leaf 5, HAC 2h, rep4


title: pal2_01_D08


title: pal2_01_D07


title: pal2_01_D05


title: pal2_01_D06


title: SCC25 Controlsh R2

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

description:
SCC25 featureCountsOutput.txt
SCC25-nonsilencingP3control

data_processing:
Base calling was done using cassava 1.5
Alignment of RNA-Seq fastq file was done using Hisat2 v2.1.0
RNA-seq alignment reads were counted using featureCounts v 1.5.3 with the following arguments -t exon -g gene_id -T 16 -p -a
Alignment of ChIP-Seq fastq file was done using bowtie v1.1.1 with the following parameters:  -m 1
Peak calling of CHIP-seq data was done using macs v 2.2.7.1 with default parametes (qvalue =0.05)
DESeq2 (v1.12.4) was used to normalize the read counts and derive TPM values were calculated according to the method of Wagner et al., Theory in Bioscience, 2012
Assembly: ncbi-hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, bigwig

source_name: SCC25 sh Control Rep 2

growth_protocol: All cells were grown in recommended media (DMEM/F12 for SCC25, DMEM for CAL27, and McCoy's 5A Iwakata and Grace Modified media) supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
(RNA-seq) All cells were harvested in Trizol and total RNA was extracted using  Direct-Zol RNA mini-prep kit (zymo research) according to manufacturer's protocol.
(ChIP-seq) A253 and SCC25 cells were grown to 80% confluency in 150 mm culture dish and cross-linked with 1% Formaldehyde for 10 minutes. The cross-linking reaction was quenched with Glycine to a final concentration of 125mM. Fixed HNSCC cells were prepared for chromatin shearing using Diagenode low Sodium Dodecyl Sulphate (SDS) shearing kit for Transcription Factors (Diagenode) and sonicated using a Diagenode Bioruptor to obtain sheared chromatin of between 200-400bp. p63 ChIP for A253 cells was performed using 2ug anti-p63 antibodies (Np631.1, and 4A4). SCC25 ChIP was performed using 2ug H129 or 3ug 4A4 antibodies. The p63 4A4 experiment in SCC25 has been previously described [37, 102]. Following immunoprecipitation, DNA-protein complex was then subjected to cross-link reversal and proteinase K treatment. Input DNA and DNA from immunoprecipitation experiments were purified and concentrated using Qiagen MinElute kit.
(RNA-seq) Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Total RNA was enriched for mRNA before library construction
(ChIP-seq) DNA libraries were prepared from concentrated DNA using ThruPLEX DNA-seq kit (Rubicon Genomics), and single-end sequencing was done on an Illumina HISeq 2500.

treatment_protocol: p63 depleted A253 and SCC25 cells were selected and maintained with 2ug/ml puromycin

value: Oral Cancer Cells

value: Control (Empty Vector)

tag: growth protocol

value: Grown in selection media (Regular Media + 2ug/ml puromycin)


title: SCC25 Controlsh R1

description:
SCC25 featureCountsOutput.txt
SCC25-nonsilencingP2control

source_name: SCC25 sh Control Rep 1


title: leaf 5, HAC 2h, rep2


title: SCC25 H129 ab

description:
SCC25 H129.bw
none

source_name: SCC25 Wild Type Cells

value: Parental Cells

tag: chip antibody

value: Grown in regular media


title: leaf 5, HAC 2h, rep1


title: SCC25 4A4 ab

description:
SCC25 4A4.bw
none


title: SCC25 sh50 R2

description:
SCC25 featureCountsOutput.txt
SCC25-24250-P3

source_name: SCC25 shp63 Rep 2

value: p63 depleted


title: SCC25 sh50 R1

description:
SCC25 featureCountsOutput.txt
SCC25-24250-P2

source_name: SCC25 shp63 Rep 1


title: A253 p63 deltaNp63 1.1 ab

description:
A253_deltaNp631.bw
none

source_name: A253 Wild Type Cells


title: leaf 4, HAC 2h, rep6

value: leaf


title: A253 TF Input R2

description:
A253 Input TF ChIP.bw
none


title: SCC25 Input

description:
SCC25 Input.bw
none


title: pal3_01_D16


title: leaf 5, HAC 2h, rep3


title: pal2_01_D01


title: pal2_01_D04


title: pal2_01_D02


title: pal2_01_D03


title: pal3_01_C24


title: leaf 4, HAC 2h, rep5


title: pal2_01_C22


title: pal2_01_C21


title: leaf 4, HAC 2h, rep1


title: A253 TF Input R1

description:
A253 Input TF ChIP.bw
none


title: leaf 4, HAC 2h, rep3


title: A253 histone Input R2

description:
A253 Input Histone.bw
none


title: A253_p63_4A4_ab

description:
A253_4A4.sorted.bam.bw
none


title: leaf 4, HAC 2h, rep4


title: A253 H3K4Me3 R2

description:
A253-H3K4me3.bw
none


title: A253 histone Input R1

description:
A253 Input Histone.bw
none


title: A253 Contrlsh R2

description:
A253 featureCountsOutput.txt
none

source_name: A253 shControl Rep2


title: A253 H3K4Me3 R1

description:
A253-H3K4me3.bw
none


title: A253 H3K27Ac R1

description:
A253-H3K27ac.bw
none


title: A253 H3K4Me1 R2

description:
A253-H3K4me1.bw
none


title: leaf 4, HAC 2h, rep2


title: leaf 6, HAC 30min, rep6

value: HAC 30 min


title: A253 50shR2

description:
A253 featureCountsOutput.txt
none


title: A253 H3K4Me1 R1

description:
A253-H3K4me1.bw
none


title: A253 H3K27Ac R2

description:
A253-H3K27ac.bw
none


title: A253 50sh R1

description:
A253 featureCountsOutput.txt
none


title: leaf 6, HAC 30min, rep5


title: pal3_01_C23

value: d/d


title: A253 48sh R1

description:
A253 featureCountsOutput.txt
none


title: A253 48sh R2

description:
A253 featureCountsOutput.txt
none


title: leaf 6, HAC 30min, rep4


title: A253 Contrlsh R1

description:
A253 featureCountsOutput.txt
none

source_name: A253 shControl Rep1


title: pal2_01_C20

value: Blastema


title: pal2_01_C19


title: pal2_01_C17


title: pal2_01_C18


title: leaf 6, HAC 30min, rep2


title: leaf 6, HAC 30min, rep3


title: leaf 6, HAC 30min, rep1


title: leaf 5, HAC 30min, rep6


title: Human skin, PPD, B14

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

data_processing:
Quality control on raw sequence data was performed with FastQC (version 0.10.0; Babraham Institute, Cambridge, United Kingdom)
Rna-seq reads were aligned with STAR-aligner using the genome build Ensembl Homo sapiens GRCh38 Release 91
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: GRCh38 build, Ensembl Release 91

source_name: Skin

extract_protocol:
The biopsy specimens were placed in RNAlater and frozen in liquid nitrogen before storage at -80°C. Total RNA was prepared from skin biopsy specimens by using the RNeasy Universal Plus Kit (Qiagen, Hilden, Germany).
Library preparation for RNA-seq was performed with the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, Calif).

treatment_protocol: Donors were patch tested with 20 mg of 1% PPD in petrolatum (100% white petrolatum, vaseline), and a vehicle petrolatum control was applied in 8-mm Finn chambers on the buttocks with an occlusion time of 48 hours. Punch biopsy specimens (4mm) were taken on day 4 from both the PPD and vehicle test sites.

value: Skin

tag: condition

value: Allergic contact dermatitis, mild

tag: subject id

value: PPD


title: Human skin, PPD, B11


title: Human skin, VAS, B9

value: Vaseline/Petrolatum


title: Human skin, VAS, B13

value: Allergic contact dermatitis, severe


title: pal2_01_C16

value: Palette


title: pal2_01_C15


title: Human skin, VAS, B8


title: Human skin, PPD, B9


title: Human skin, PPD, B8


title: MCCC1_rep2_INPUT

value: Human embryonic kidney

value: MCCC1-V5 overexpressed


title: Human skin, VAS, B14


title: pal2_01_C14


title: Human skin, VAS, B7


title: Human skin, PPD, B7


title: pal2_01_C13


title: Human skin, VAS, B5


title: Human skin, VAS, B4


title: Human skin, PPD, B5


title: leaf 5, HAC 30min, rep3


title: leaf 5, HAC 30min, rep4


title: pal2_01_C12


title: Human skin, VAS, B11


title: Human skin, PPD, B13


title: leaf 5, HAC 30min, rep5


title: Human skin, VAS, B3


title: Human skin, PPD, B4


title: leaf 5, HAC 30min, rep2


title: pal2_01_C11


title: leaf 5, HAC 30min, rep1


title: Human skin, PPD, B3


title: Human skin, VAS, A11

value: hairdressers without contact dermatitis, nonresponder


title: leaf 4, HAC 30min, rep6


title: Human skin, PPD, A11


title: Human skin, VAS, A10


title: pal2_01_C09


title: pal2_01_C08


title: Human skin, PPD, A10


title: Human skin, PPD, A8


title: pal2_01_C07


title: leaf 4, HAC 30min, rep4


title: Human skin, VAS, A7


title: pal2_01_C10


title: leaf 4, HAC 30min, rep3


title: Human skin, VAS, A4


title: Human skin, VAS, A8


title: pal2_01_C06


title: Human skin, PPD, A7


title: leaf 4, HAC 30min, rep2


title: Human skin, VAS, A3


title: pal2_01_C05


title: Human skin, PPD, A4


title: Human skin, PPD, A3


title: leaf 4, HAC 30min, rep1


title: leaf 6, control, rep6

value: control


title: Human skin, VAS, A2


title: pal2_01_C04


title: leaf 6, control, rep4


title: leaf 6, control, rep5


title: pal2_01_C02


title: pal2_01_C03


title: MDA-MB-231_siEZ-Control_RNA_Rep2

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Reads were filtered for adaptor contamination using cutadapt (Martin, 2011) and filtered such that at least 90% of bases of each read had a quality score > 20
Reads were aligned to the reference genome (hg19) using STAR version 2.5.2b retaining only primary alignments (Dobin et al., 2013). Reads overlapping blacklisted regions of the genome were then removed
Transcript abundance was then estimated using salmon (Patro et al., 2017b), and differential expression was detected using DESeq2 (Love et al., 2014).
Assembly: hg19
Supplementary files format and content: bigWig files for input control and ChIP samples have been normalized to the total number of aligned reads
Supplementary files format and content: VST-normalized gene expression data matrix (siEZH2 RNA-seq)
Supplementary files format and content: Raw gene count matrix (siRel RNA-seq)

growth_protocol: SUM149 or MDA-MB-231 cells were seeded and allowed to adhere in 10cm dishes for passaging.

extract_protocol:
RNA was extracted from SUM149 and MDA-MB-231 cells using RNeasy kit with on-column DNase digestion (QIAGEN)
Libraries were prepared for high-throughput sequencing by the UNC High-throughput Sequencing Facility as per manufacturer's recommendations

treatment_protocol: Transfection was performed with Dharmafect I (Dharmacon) for siRNA (20nM, see Key Resources Table) or FuGene HD (Promega) for plasmids (0.75g/mL, see Key Resources Table) prepared in OptiMEM (Gibco). Cells were harvested 48 hours after transfection unless otherwise indicated. Lentivirus was prepared using the psPAX2 and pMD2.5G packaging system co-transfected for 48 hours in HEK293T cells. Supernatant containing virus was passed through 0.45uM filters (Pall Corporation), and applied to target cells with 8ug/mL polybrene (EMD Millipore). Stable cell lines were further selected using 1ug/mL puromycin (Thermo Fisher Scientific) or Geneticin (Gibco) for 7 days before validation.

value: siControl

tag: replicate


title: leaf 6, control, rep2


title: SUM149_siEZ-Control_RNA_Rep2


title: pal2_01_C01


title: pal1_01_B24


title: MDA-MB-231_siEZ-Control_RNA_Rep1


title: SUM149_siEZH2_RNA_Rep2


title: MDA-MB-231_siEZH2_RNA_Rep2


title: MDA-MB-231_siEZH2_RNA_Rep1


title: leaf 6, control, rep3


title: pal1_01_B23


title: SUM149_siEZH2_RNA_Rep1


title: Blood_Platelets_VUMC-Vumc-913-NSCLC

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Assembly: hg19
Supplementary files format and content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

value: Thrombocytes

tag: diagnosis

value: NSCLC

value: nonResponder


title: leaf 6, control, rep1

value: leaf


title: Blood_Platelets_VUMC-Vumc-1941-NSCLC


title: pal2_01_B22

value: d/d


title: leaf 5, control, rep6


title: Human skin, PPD, A2


title: leaf 4, HAC 30min, rep5

value: HAC 30 min


title: Blood_Platelets_VUMC-Vumc-1863-NSCLC

value: Responder


title: Blood_Platelets_VUMC-Vumc-1867-NSCLC


title: Blood_Platelets_VUMC-Vumc-1773-NSCLC


title: SUM149_siEZ-Control_RNA_Rep1


title: Blood_Platelets_VUMC-Vumc-1740-NSCLC


title: leaf 5, control, rep5


title: pal2_01_B21

value: Blastema


title: Blood_Platelets_VUMC-Vumc-1702-NSCLC


title: leaf 5, control, rep4


title: Blood_Platelets_VUMC-Vumc-1638-NSCLC


title: pal2_01_B20


title: pal2_01_B19


title: Blood_Platelets_VUMC-Vumc-1617-NSCLC


title: Blood_Platelets_VUMC-Vumc-1588-NSCLC


title: Blood_Platelets_VUMC-VUmc-1576-NSCLC


title: pal2_01_B18


title: Blood_Platelets_VUMC-Vumc-1556-NSCLC


title: pal2_01_B17


title: Blood_Platelets_VUMC-Vumc-1601-NSCLC


title: Blood_Platelets_VUMC-Vumc-1457-NSCLC


title: Blood_Platelets_VUMC-vumc-1529-NSCLC


title: leaf 5, control, rep3


title: leaf 5, control, rep2


title: leaf 5, control, rep1


title: leaf 4, control, rep6


title: Blood_Platelets_VUMC-Vumc-1250-NSCLC


title: pal2_01_B16


title: pal2_01_B15


title: Blood_Platelets_VUMC-Vumc-1086-NSCLC


title: Blood_Platelets_VUMC-Vumc-1160-NSCLC


title: leaf 4, control, rep5


title: pal2_01_B14


title: Blood_Platelets_Vumc-NSCLC-848


title: Blood_Platelets_Vumc-NSCLC-845


title: Blood_Platelets_Vumc-NSCLC-879


title: pal2_01_B13


title: leaf 4, control, rep4


title: Blood_Platelets_Vumc-NSCLC-843


title: Blood_Platelets_Vumc-NSCLC-821


title: Blood_Platelets_Vumc-NSCLC-757


title: leaf 4, control, rep2


title: Blood_Platelets_Vumc-NSCLC-756


title: Blood_Platelets_Vumc-NSCLC-749


title: leaf 4, control, rep1


title: pal2_01_B11


title: pal2_01_B10


title: Blood_Platelets_Vumc-NSCLC-717


title: Blood_Platelets_Vumc-NSCLC-724


title: Blood_Platelets_Vumc-NSCLC-611


title: pal2_01_B08


title: Blood_Platelets_Vumc-NSCLC-604


title: pal2_01_B07


title: Blood_Platelets_Vumc-NSCLC-598