title: Patient_47_F_Tm

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RBG12470_ME-Transformed

status: Public on Feb 07 2020

type: SRA

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Raw reads were aligned to Mus musculus genome (GRCm38.81) using G-SNAP (version 2015-09-29) with the following parameters: –B 5 –n 1 –N 1 –Q. HTSeq-count (version 0.6.0) was run to assign mapped reads to Ensembl genes (GRCm38.81).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: Hoxb8 Cell line

growth_protocol: Conditionally immortalised early hematopoietic progenitor cells (Hoxb8-FL cells) (Redecke et al., 2013) were cultured in RPMI 1640 medium (Sigma-R8758) supplemented with 10% Fetal Bovine Serum (FBS) (HyCloneTM GE Healthcare), 5% Flt3L conditional medium, 1% Penicillin/Streptomycin (Sigma-P0781), 1% L-Glutamine (Sigma-G7513), 0.1% 2-Mercaptoethanol (50mM stock)(Gibco®), 0.001% β-estradiol (10mM stock) at 37 ̊C and 5% CO2.

extract_protocol:
GFP positive and DAPI negative cells were FACS sorted into individual wells of a 96 well plates containing lysis buffer and processed using Smart-Seq2 protocol as previously described (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 4000.
Libraries were prepared using the Illumina Nextera XT Libraries were prepared using the Illumina Nextera XT DNA preparation kit.

tag: treatment

value: Immort

tag: day

tag: batch

tag: condition

value: ME-Transformed


title: Patient_47_E_Tm

type: RNA

city: Toronto

first: Igor

last: Jurisica

state: Ontario

address: 60 Leonard Avenue

department: Krembil Research Institute

country: Canada

institute: University Health Network

hyb_protocol: As described in Reis et al. 2011 [PMID: 21549012]

scan_protocol: According to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)

data_processing: Raw data extracted from the RCC files were assembled into matrix

label: biotin

organism: Homo sapiens

source_name: Tumour

label_protocol: Using 400 ng total RNA, gene transcrpts levels were assayed using Nanostring nCounter assay kits by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA).

extract_protocol: RNA from FFPE samples was isolated using the RecoverAll Total Nucleic Acid Isolation kit (Ambion/Life Technologies, Carlsbad, CA, USA), following our previously reported protocol with modifications to improve RNA yield [PMID: 23835716]. RNA was stored at -80ºC until RNA extraction

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: former

value: N

value: Tongue SCC

tag: Stage

tag: grade

value: poor

value: left ND, left hemiglossectomy

tag: rtx

tag: qtx

value: no recurrence


title: Patient_47_F_Nr

source_name: Normal

tag: drinker

tag: pathology report

value: Anterior margin

tag: tumor size at maximum dimension

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: RBG12437_MLLENL-BM

tag: treatment

tag: day

value: MLLENL-BM


title: Patient_47_I_Tm

tag: batch

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_47_E_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: Stage


title: RBG12473_ME-Transformed

tag: condition


title: RBG12435_MLLENL-BM


title: RBG12436_MLLENL-BM


title: Patient_46_N_Nr

value: M

value: current

tag: drinker

value: Y

tag: pathology report

value: Dorsal aspect

tag: tumor size at maximum dimension

tag: grade

value: well

value: left ND, left partial glossectomy & FOM

tag: rtx

tag: qtx


title: Patient_46_O_Nr

tag: batch

value: Ventral aspect

tag: treatment

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence


title: Patient_47_D_Tm

tag: patient id

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Reanalysis Brx-139-1

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The paired-end reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
The number of reads aligning to each gene was then determined using htseq-count.
Samples that had fewer than 100,000 reads were discarded. Samples for which PTPRC expression was greater than 10 reads-per-million were deemed possible white blood cells and were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows).

source_name: candidate CTC

extract_protocol:
Single CTCs were isolated from fresh whole blood following leukocyte depletion using the microfluidic CTC-iChip as described in PMID 23552373. Single cells were individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer, and flash frozen in liquid nitrogen.
Clontech SMARTer Ultra Low Input Kit for RNA v3 for cDNA synthesis and the Nextera XT kit for library construction

tag: patient

tag: clinical hormone receptor

value: HR-

tag: clinical her2

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: Patient_46_M_Tm

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Tongue and FOM SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx


title: RBG12434_MLLENL-BM

tag: treatment

value: Immort

tag: day

tag: batch

tag: condition


title: BRx-129-5--9-29

tag: patient

tag: clinical hormone receptor

value: fail


title: Patient_46_M_Nr

tag: patient id

value: Posterior margin

value: N

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_46_O_Tm

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: no recurrence


title: Patient_46_L_Nr

tag: batch

tag: patient id

value: Anterior margin

tag: treatment

tag: rtx


title: BRx-152-1

tag: patient

tag: number uniquely mapped reads

tag: ptprc expression


title: Patient_46_J_Tm

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: BRx-129-3--9-29

tag: clinical hormone receptor

tag: clinical her2


title: RA5519B-4N: Treated Rheumatoid Arthritis patient CD4nai 19

city: Oslo

first: Kari

last: Guderud

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

description: MSP1 fragmented DNA

library_source: genomic

data_processing:
Primary base calling and quality scoring was performed using BSMAP v.2.90 (-p4, -D C-CGG, -v2, -n1, -q28)
getting methylation ratios in methratio.py with samtools
Getting CGs: grep -c "CG" sorted_*.txt
Methratio format to RnBeads format were transformed with a custom R-script
Call methylation differences: RnBeads v.1.10.8  No SNPs, cov treshold=10, min.group.size=5, no sex chromosomes)
Genome_build: hg19

molecule: genomic DNA

source_name: CD4+ naïve t cell

extract_protocol:
RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
Diagenode RRBS, In house mRRBS

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Treated Rheumatoid Arthritis

tag: replicate


title: RBG12433_MLLENL-BM

tag: treatment

tag: day

tag: batch

tag: condition

value: MLLENL-BM


title: BRx-139-2

tag: patient

tag: number uniquely mapped reads

tag: ptprc expression


title: RBG12432_MLLENL-BM


title: Patient_45_S_Tm

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: FOM, tongue and palate SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

value: left ND, left parotidectomy, composite resection, free forearm flap

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of death


title: Patient_46_J_Nr

tag: batch

value: M

value: Normal tissue

value: well

tag: treatment

value: left ND, left partial glossectomy & FOM

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up


title: RBG12431_MLLENL-BM

value: Immort

tag: day

tag: condition


title: RA5518B-4N: Treated Rheumatoid Arthritis patient CD4nai 18

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: Patient_45_R_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

value: N

value: no recurrence


title: Reanalysis Brx-129-2--9-29

tag: patient

tag: clinical hormone receptor

value: HR-

tag: clinical her2

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: RA5517BK-4N: Treated Rheumatoid Arthritis patient CD4nai 17

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Treated Rheumatoid Arthritis


title: RBG12430_MLLENL-BM

tag: treatment

tag: day

tag: batch

tag: condition

value: MLLENL-BM


title: BRx-110-3--9-8

value: HR+


title: BRx-110-2--9-8


title: RBG12429_MLLENL-BM


title: Patient_45_R_Nr

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: Superior medial soft palate margin

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RA5516B-4N: Treated Rheumatoid Arthritis patient CD4nai 16

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: BRx-129-4--9-29

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

value: fail

tag: ptprc expression


title: Patient_45_Q_Tm

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: FOM, tongue and palate SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

tag: treatment

value: left ND, left parotidectomy, composite resection, free forearm flap

tag: rtx

tag: qtx


title: RA5515B-4N: Treated Rheumatoid Arthritis patient CD4nai 15

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: Patient_45_Q_Nr

tag: batch

value: Superior margin

value: N

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: BRx-110-1--9-8

tag: patient

tag: clinical hormone receptor

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: RA5514B-4N: Treated Rheumatoid Arthritis patient CD4nai 14

description: MSP1 fragmented DNA

tag: tissue


title: BRx-10--9-29


title: Patient_45_P_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: rtx

tag: qtx

value: no recurrence


title: RA5513B-4N: Treated Rheumatoid Arthritis patient CD4nai 13

description: MSP1 fragmented DNA

tag: library prep kit

tag: disease state

tag: replicate


title: RBG12426_MLLENL-BM

value: Immort

tag: day

tag: batch

tag: condition


title: RBG12427_MLLENL-BM


title: RA5512B-4N: Treated Rheumatoid Arthritis patient CD4nai 12

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell


title: BRx-102-2

tag: patient

tag: number uniquely mapped reads

value: pass

tag: ptprc expression


title: Patient_45_P_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Anterior lateral margin

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_45_O_Tm

tag: batch

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: rtx

tag: qtx


title: RA5511B-4N: Treated Rheumatoid Arthritis patient CD4nai 11

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Treated Rheumatoid Arthritis

tag: replicate


title: BRx-129-1--9-29

tag: patient

tag: clinical hormone receptor

value: HR-

tag: clinical her2

tag: number uniquely mapped reads

tag: ptprc expression


title: RBG12424_MLLENL-BM

tag: day

tag: condition

value: MLLENL-BM


title: Patient_45_O_Nr

tag: batch

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: Anterior margin

tag: tumor size at maximum dimension

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RBG12428_MLLENL-BM

tag: treatment

tag: day


title: RA5510B-4N: Treated Rheumatoid Arthritis patient CD4nai 10

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: input.bam.bigwig

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

description: genomic DNA enriched following ERRgamma chromatin immunoprecipitation

data_processing:
Sequences were aligned to the human genome database (Hg19) using BWA v0.5.9 (Li and Durbin, 2009)
Significant DNA binding (peak) was determined using MACS v1.4.1 software (Zhang et al., 2008).
Peak annotation, tag directory, bed file generation, and de novo motif discovery were performed with the Homer package v3.18.
Genome_build: hg19
Independent .bigwig files for each ChIP-seq sample are provided along with an excel file of the annotated ERRgamma peaks following the merge of duplicate samples versus input DNA as a control. Additionnally, raw .fastq files for each sample are provided in which duplicate sequencing runs (eg S1, S2) for each ERRg ChIP-seq replicate were performed.

source_name: BT-474 human breast cancer cell line treated with vehicle for 90 minutes

growth_protocol: Cells were cultured in regular DMEM. 24h after seeding, media was changed and fresh media was added.

extract_protocol:
After 90min following media renewal, nuclei were isolated and subjected to chromatin immunoprecipitation. Following ERRgamma ChIP, genomic DNA was purified with QIAGEN DNA extraction kit.
Libraries were performed at the Génome Québec Innovation Centre (McGill University) using standard protocol for HiSeq - Illumina Single reads 50bp sequencing lane

value: Breast tumor cell line

tag: chip antibody

value: input DNA

tag: chip-antibody

value: input DNA as control ChIP-seq


title: RBG12423_MLLENL-BM

tag: batch

tag: condition


title: ERRg_ChIP-seq2.bam.bigwig

value: ERRg antibody (custom antibody, Dr. Ron Evans lab)

value: genomic DNA enriched following ERRgamma chromatin immunoprecipitation


title: Patient_45_M_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Medial margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

value: left ND, left parotidectomy, composite resection, free forearm flap

tag: rtx

value: N

tag: qtx

tag: recurrence status

value: no recurrence


title: ERRg_ChIP-seq1.bam.bigwig

tag: tissue


title: RA5509B-4N: Treated Rheumatoid Arthritis patient CD4nai 9

description: MSP1 fragmented DNA

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Treated Rheumatoid Arthritis

tag: replicate


title: Patient_45_L_Tm

tag: batch

value: F

value: FOM, tongue and palate SCC

tag: treatment

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: RBG12422_MLLENL-BM

value: Immort

tag: day

tag: condition

value: MLLENL-BM


title: RA5508B-4N: Treated Rheumatoid Arthritis patient CD4nai 8

description: MSP1 fragmented DNA


title: RBG12421_MLLENL-BM


title: Patient_45_L_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx


title: RBG12425_MLLENL-BM

tag: treatment

tag: batch


title: RBG12420_MLLENL-BM


title: Patient_45_K_Tm

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: BRx-102-1

tag: patient

tag: number uniquely mapped reads

value: pass

tag: ptprc expression

value: fail


title: RBG12419_MLLENL-BM

tag: day

tag: condition


title: Patient_45_K_Nr

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: last follow-up

tag: date of death


title: RA5506B-4N: Treated Rheumatoid Arthritis patient CD4nai 6

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: RA5505B-4N: Treated Rheumatoid Arthritis patient CD4nai 5

description: MSP1 fragmented DNA


title: RBG12418_MLLENL-BM

tag: treatment

tag: batch


title: Patient_44_J_Tm

value: M

value: never

value: Tongue SCC

tag: Stage

tag: grade

value: left ND, resection oral cavity & oropharynx ca, free forearm flap

tag: rtx

tag: qtx

tag: recurrence status

value: regional recurrence-ipsilateral

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RA5503B-4N: Treated Rheumatoid Arthritis patient CD4nai 3

description: MSP1 fragmented DNA


title: Patient_44_I_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

value: N

tag: pathology report

tag: tumor size at maximum dimension

value: moderate

tag: last follow-up


title: Patient_44_I_Nr

tag: batch

value: Lateral FOM

tag: Stage

tag: treatment

tag: date of death


title: RBG12416_MLLENL-BM

tag: day

tag: condition


title: RBG12417_MLLENL-BM


title: RBG12415_MLLENL-BM


title: RA5502B-4N: Treated Rheumatoid Arthritis patient CD4nai 2

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Treated Rheumatoid Arthritis

tag: replicate


title: 6_Day 6 TGF-b Polysome

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: CEL files were processed by the RMA method as implemented by the rma function of the oligo package of R/Bioconductor.

source_name: MCF10A cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: MCF10A were grown as previously described [PUBMED ID 12798140].

extract_protocol: Polysome fractions were combined and RNA isolated with TRIzol reagent.

treatment_protocol: MCF10A cells were split the day before initiating treatment with TGF-beta (5ng/mL) for 3 days and then harvested or split and re-treated with TGF-beta for a total of 6 days.Untreated control cells and TGF-beta treated cells were harvested for RNA.

tag: cell line

value: breast cancer

value: 6 days TGF-b

tag: molecule subtype

value: Polysome


title: Patient_44_H_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: grade

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RBG12414_MLLENL-BM

tag: treatment

value: Immort

tag: day

tag: batch

tag: condition

value: MLLENL-BM


title: Patient_44_H_Nr

tag: drinker

tag: pathology report

value: Adjacent soft palate

tag: tumor size at maximum dimension

tag: Stage

tag: last follow-up

tag: date of death


title: 5_Day 3 TGF-b Polysome

tag: cell line

tag: tissue

value: 3 days TGF-b

tag: molecule subtype


title: RA5507B-4N: Treated Rheumatoid Arthritis patient CD4nai 7

description: MSP1 fragmented DNA

tag: library prep kit

tag: disease state

tag: replicate


title: RA5111K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 11.2

description: MSP1 fragmented DNA

value: Newly diagnosed Rheumatoid Arthritis


title: p16.52 Tomato

city: Lausanne

first: sophie

last: croizier

address: Genopode building

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus genome (GRCm38)  using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using  Ensembl version 92 gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read counts

source_name: FACS isolated Hypothalamic neurons

extract_protocol:
RNA were extracted using picopure extraction kit (Thermofischer)
500 picograms of RNAs were reverse transcript using SMART-Seq v4 Ultra Low Input RNA (Takara) and RNA-seq librairies were prepared the Illumina Nextera XT DNA Library kit (Illumina). A sequencing depth of 98-138 millions of reads was used per library.

tag: cell types

value: Hypothalamic POMC progenitors that do not give rise to NPY neurons

tag: age

value: postnatal day P16

tag: strain


title: RA5111B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 11.1

description: MSP1 fragmented DNA


title: p16.51 Tomato


title: RBG12413_MLLENL-BM

tag: treatment

tag: day

tag: batch


title: Patient_44_G_Tm

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: never

tag: drinker

tag: pathology report

value: Tongue SCC

tag: grade

value: left ND, resection oral cavity & oropharynx ca, free forearm flap

tag: rtx

tag: qtx

tag: recurrence status

value: regional recurrence-ipsilateral

tag: date of diagnosis

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: p16.303 DP

tag: cell types

value: POMC progenitors giving rise to NPY neurons

tag: age

tag: strain


title: 4_Untreated Polysome

tag: cell line

tag: tissue

tag: treatment

tag: molecule subtype


title: RBG12412_MLLENL-BM

tag: day

tag: batch

tag: condition


title: 1_Untreated Total mRNA

value: mRNA


title: RA5110K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 10.2

description: MSP1 fragmented DNA

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

tag: replicate


title: 3_Day 6 TGF-b Total mRNA

value: breast cancer

value: 6 days TGF-b


title: p16.301 DP


title: RA5501B-4N: Treated Rheumatoid Arthritis patient CD4nai 1

description: MSP1 fragmented DNA

value: Treated Rheumatoid Arthritis


title: Patient_44_F_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

value: N

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

tag: rtx

tag: qtx

tag: recurrence status

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: RBG12411_MLLENL-BM

tag: treatment

value: Immort

tag: day

tag: batch

tag: condition

value: MLLENL-BM


title: RA5110B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 10.1

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate


title: 2_Day 3 TGF-b Total mRNA

tag: cell line

value: 3 days TGF-b

tag: molecule subtype


title: RA5109K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 9.2

description: MSP1 fragmented DNA


title: p16.200 gfp

tag: cell types

value: Hypothalamic NPY-GFP+ neurons

tag: age

value: postnatal day P16

tag: strain


title: RBG12409_MLLENL-BM


title: RA5109B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 9.1

description: MSP1 fragmented DNA


title: Patient_44_E_Nr

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: never

tag: drinker

tag: pathology report

value: Medial margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: left ND, resection oral cavity & oropharynx ca, free forearm flap

tag: rtx

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RA5108B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 8.1

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

tag: disease state

tag: replicate


title: p16.1.2.3.DP

tag: cell types

value: POMC progenitors giving rise to NPY neurons

tag: age

tag: strain


title: p16.10 gfp


title: RBG12408_MLLENL-BM

tag: treatment

tag: day

tag: batch

tag: condition


title: Patient_44_C_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Tongue SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

value: regional recurrence-ipsilateral

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: RA5107K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 7.2

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

tag: replicate


title: Patient_44_E_Tm

tag: batch

tag: patient id

value: N

tag: treatment

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_44_G_Nr

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Posterior and deep margins

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate


title: RBG12407_MLLENL-BM

value: Immort

tag: day

tag: condition

value: MLLENL-BM


title: Patient_44_C_Nr

tag: batch

tag: patient id

value: Anterior margin

tag: rtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: p16.103 Tomato

tag: cell types

value: Hypothalamic POMC progenitors that do not give rise to NPY neurons

tag: age

tag: strain


title: Patient_43_U_Tm

tag: gender

tag: age at diagnosis

tag: smoker

value: former

value: Y

value: Maxillary SCC

value: well

tag: treatment

value: right ND, right partial maxillectomy

tag: qtx

tag: recurrence status

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: p14.41 DP

value: POMC progenitors giving rise to NPY neurons

value: postnatal day P14


title: RBG11913_ME-Parental

value: Untreated

tag: day

tag: batch

tag: condition

value: ME-Parental


title: RA5107B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 7.1

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate


title: RA5106B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 6.1

description: MSP1 fragmented DNA


title: p16.2 gfp

tag: cell types

value: Hypothalamic NPY-GFP+ neurons

tag: age

value: postnatal day P16

tag: strain


title: RBG12410_MLLENL-BM

value: Immort

value: MLLENL-BM


title: p14.40 Tomato

value: Hypothalamic POMC progenitors that do not give rise to NPY neurons


title: RA5105K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 5.2

description: MSP1 fragmented DNA


title: RBG11905_ME-Parental


title: Patient_43_M_Tm

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: former

tag: drinker

value: Y

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

value: N

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: Patient_43_M_Nr

tag: batch

value: Posterior margin

value: well

tag: treatment

value: right ND, right partial maxillectomy

tag: qtx

tag: recurrence status

value: no recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RBG11901_ME-Parental

value: Untreated

tag: day

tag: condition

value: ME-Parental


title: p14.400.401 DP

tag: cell types

value: POMC progenitors giving rise to NPY neurons

tag: age

value: postnatal day P14

tag: strain


title: RA5104B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 4.1

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate


title: RA5105B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 5.1

description: MSP1 fragmented DNA


title: Patient_43_L_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Maxillary SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: RBG11900_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition


title: p14.2 Tomato

tag: cell types

value: Hypothalamic POMC progenitors that do not give rise to NPY neurons

tag: age

tag: strain


title: RBG11896_ME-Parental


title: RBG12406_MLLENL-BM

value: Immort

value: MLLENL-BM


title: RA5103B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 3.1

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: Patient_42_S_Tm

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

tag: pathology report

value: Oral SCC

tag: tumor size at maximum dimension

tag: Stage

value: moderate

value: bilat ND, resection oral cavity ca, free forearm flap

tag: qtx

tag: recurrence status

value: local recurrence

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RA5103K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 3.2

description: MSP1 fragmented DNA

tag: tissue


title: p14.33 gfp

tag: cell types

value: Hypothalamic NPY-GFP+ neurons

tag: age

tag: strain


title: Patient_43_U_Nr

tag: batch

tag: patient id

value: former

value: Y

value: Posterior margin

tag: grade

value: well

tag: treatment

value: right ND, right partial maxillectomy

tag: rtx

value: N

value: no recurrence

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: p14.2 gfp

value: postnatal day P14


title: Patient_42_R_Nr

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

value: Medial inferior margin

tag: tumor size at maximum dimension

tag: Stage

tag: qtx


title: Patient_42_Q_Tm

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: RBG11893_ME-Parental

tag: treatment

value: Untreated

tag: day

tag: batch

tag: condition

value: ME-Parental


title: RA5102B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 2.1

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate


title: p14.1 Tomato

tag: cell types

value: Hypothalamic POMC progenitors that do not give rise to NPY neurons

tag: age

tag: strain


title: RBG11886_ME-Parental


title: RBG11887_ME-Parental


title: p14.40 DP

value: POMC progenitors giving rise to NPY neurons


title: Patient_42_Q_Nr

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

tag: pathology report

value: Medial superior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

value: bilat ND, resection oral cavity ca, free forearm flap

tag: rtx

value: local recurrence

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: RA5102K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 2.2

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: RA5101K3-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 1.2

description: MSP1 fragmented DNA


title: RBG11884_ME-Parental

tag: treatment

tag: day

tag: batch

tag: condition


title: Patient_47_H_Nr

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: former

tag: drinker

value: N

value: Superior margin

value: poor

value: left ND, left hemiglossectomy

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_42_P_Tm

tag: pathology report

value: Oral SCC

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: rtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: RA5101B-4N: Newly diagnosed Rheumatoid Arthritis patient CD4nai 1.1

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

tag: replicate


title: IRC5109A-4N: Control CD4nai 9

description: MSP1 fragmented DNA

value: Healthy control


title: Patient_42_O_Tm

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

value: Oral SCC (it does not specify exact site)

tag: treatment

tag: qtx


title: Patient_42_P_Nr

value: M

tag: pathology report

value: Medial posterior margin

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: recurrence status

tag: date of 1st recurrence

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: Patient_42_O_Nr

value: current

value: Medial anterior margin

tag: rtx

tag: date of diagnosis

tag: last follow-up

tag: date of death


title: IRC5111A-4N: Control CD4nai 11

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: lnCN30D9 [BGISEQ-500]

city: Xuzhou

first: Zuobin

last: Zhu

state: Jiangsu

address: Tongshan road 209

department: Department of Genetics

institute: Xuzhou Medical University

data_processing:
The impurities of raw data are 5' primer contaminants, no insert tags, oversized insertion, low quality tags, poly A tags and small tags were filered  from the FASTQ file and get the final clean tags.
After filtering, clean tags were mapped to sRNA database.
We use miRDeep 2 to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated sRNA tags which could be mapped to the genome.
The small RNA expression level is calculated by using TPM
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Caenorhabditis elegans

source_name: Whole cell tissue

growth_protocol: C. elegans were fed E. coli OP50 at 20 °C on normal growth medium (NGM).

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. Subsequently, total RNA was qualified and quantified using a NanoDrop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

tag: strain

tag: genotype

value: trans-nuclear

tag: age

value: day 9


title: lnCN30D12 [BGISEQ-500]

value: day 12


title: lnCN30D6  [BGISEQ-500]

value: day 6


title: lnCN30D0A3  [BGISEQ-500]

value: day 0


title: IRC5110A-4N: Control CD4nai 10

description: MSP1 fragmented DNA


title: mTECs_from_WT_mice_ATAC-seq_2

city: bunkyo

first: Yoshihiko

last: Tomofuji

state: Tokyo

address: hongo 7-3-1

department: Immunology

country: Japan

institute: University of Tokyo

description:
ATAC_WT_2
ATAC-seq for mTECs from WT mice
processed data file: ATAC_WT.bw

data_processing:
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 ver2.3.2.
Duplicates were removed through command line interface.
Generated sam files were converted to bamfiles by using samtools.
bamfiles were converted to bigwig files by using deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files

source_name: mTECs

extract_protocol:
5×10e4 mTEChi from 3- to 4-week-old male WT mice, Fezf2fl/fl Foxn1-Cre mice, or Chd4fl/fl Foxn1-Cre mice were used for preparation of ATAC-seq libraries.
Cells were suspended in 100 µl of cold hypotonic lysis buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP40], followed by immediate centrifugation at 550 g for 30 min. The pellet was re-suspended in 5 µl of transposition reaction mix [1 µl of Tagment DNA Enzyme and 2.5 µl of Tagment DNA Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5 µl H2O], and was incubated for 60 min at 37 °C for DNA to be fragmented and tagged. For library preparation, two sequential seven-cycles of PCR were performed to enrich small tagmented DNA fragments. After the PCR, the libraries were selected for large fragments (more than 100 bp) using AMPure XP.

tag: genotype/variation

value: WT

tag: Sex

value: Male

tag: cell type

value: TECs


title: mTECs_from_WT_mice_ATAC-seq_1

description:
ATAC_WT_1
ATAC-seq for mTECs from WT mice
processed data file: ATAC_WT.bw


title: mTECs_from_Fezf2cKO_mice_ATAC-seq_1

description:
ATAC_Fezf2cKO_1
ATAC-seq for mTECs from Fezf2 fl/fl Foxn1 Cre (Foxp3-GFP) mice
processed data file: ATAC_Fezf2cKO.bw


title: lnCN30D0A2  [BGISEQ-500]


title: Patient_41_P_Nr

tag: batch

tag: patient id

tag: gender

value: F

tag: age at diagnosis

tag: smoker

value: former

tag: drinker

value: Y

tag: pathology report

value: Right and left soft tissue margins

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

tag: treatment

value: left ND, composite resection, free forearm flap

value: N

tag: qtx

tag: recurrence status

value: local recurrence

tag: date of 1st recurrence


title: p14.1 gfp

tag: cell types

value: Hypothalamic NPY-GFP+ neurons

tag: age

value: postnatal day P14

tag: strain


title: IRC5107A-4N: Control CD4nai 7

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Healthy control

tag: replicate


title: Patient_41_O_Tm

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

value: Tongue SCC

tag: rtx

tag: date of diagnosis

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: mTECs_from_Fezf2-3Flag_KI_mice_Input_2

description:
ChIP_M2_input_2
processed data file: ATAC_Chd4cKO.bw

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 ver2.3.2.
Duplicates were removed through command line interface.
Generated sam files were converted to bamfiles by using samtools.
bamfiles were converted to bigwig files by using deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files

extract_protocol: Not provided

tag: genotype/variation

tag: cell type

tag: chip antibody

value: input


title: mTECs_from_Fezf2cKO_mice_ATAC-seq_2

description:
ATAC_Fezf2cKO_2
ATAC-seq for mTECs from Fezf2 fl/fl Foxn1 Cre (Foxp3-GFP) mice
processed data file: ATAC_Fezf2cKO.bw

tag: strain

tag: Sex

value: Male


title: IRC5104A-4N: Control CD4nai 4

description: MSP1 fragmented DNA

tag: tissue

tag: library prep kit

tag: disease state

tag: replicate


title: Patient_41_N_Tm

tag: batch

tag: patient id

tag: gender

tag: age at diagnosis

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

tag: qtx

tag: recurrence status

tag: date of 1st recurrence


title: lnN2D12  [BGISEQ-500]

tag: strain

tag: genotype

value: wild type

tag: age

value: day 12


title: lnCN30D0A1  [BGISEQ-500]

value: trans-nuclear

value: day 0


title: mTECs_from_Fezf2-3Flag_KI_mice_Input_1

description:
ChIP_M2_input_1
processed data file: ATAC_Chd4cKO.bw

tag: genotype/variation

tag: cell type

value: TECs

tag: chip antibody


title: Patient_40_G_Tm

tag: batch

tag: patient id

tag: gender

value: M

tag: smoker

value: current

value: Y

value: moderate

value: left partial glossectomy

tag: rtx

value: regional recurrence-ipsilateral

tag: date of diagnosis

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: Patient_41_M_Tm

value: F

tag: age at diagnosis

value: former

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: Stage

tag: grade

tag: treatment

value: left ND, composite resection, free forearm flap

value: N

tag: qtx

tag: recurrence status

value: local recurrence

tag: date of 1st recurrence


title: lnN2D9  [BGISEQ-500]

tag: strain

tag: genotype

tag: age

value: day 9


title: mTECs_from_Fezf2-3Flag_KI_mice_IgG_ChIP_2

description:
ChIP_M2_IgG_2
processed data file: ATAC_Fezf2cKO.bw

tag: genotype/variation

tag: cell type

tag: chip antibody

value: IgG (control)


title: IRC5102A-4N: Control CD4nai 2

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Healthy control

tag: replicate


title: IRC5106A-4N: Control CD4nai 6

description: MSP1 fragmented DNA


title: IRC5101A-4N: Control CD4nai 1

description: MSP1 fragmented DNA


title: mTECs_from_Fezf2-3Flag_KI_mice_IgG_ChIP_1

description:
ChIP_M2_IgG_1
processed data file: ATAC_Fezf2cKO.bw

value: TECs


title: lnN2D0A3  [BGISEQ-500]

value: wild type

value: day 0


title: mTECs_from_Fezf2-3Flag_KI_mice_anti_Flag_ChIP_2

description:
ChIP_M2_Fezf2_2
processed data file: ATAC_WT.bw

value: anti-Flag tag


title: Patient_40_F_Tm

tag: batch

tag: patient id

tag: gender

value: M

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: Tongue SCC

tag: tumor size at maximum dimension

value: moderate

tag: rtx

tag: date of diagnosis

tag: date of 2nd recurrence

tag: date of 3rd recurrence

tag: last follow-up

tag: date of death


title: lnN2D0A2  [BGISEQ-500]

tag: strain

tag: genotype

tag: age


title: Patient_40_G_Nr

tag: batch

value: adjacent normal

tag: Stage

tag: grade

tag: treatment

value: left partial glossectomy

tag: qtx

tag: recurrence status

value: regional recurrence-ipsilateral

tag: date of 1st recurrence


title: RA5108B-4m: Newly diagnosed Rheumatoid Arthritis patient CD4mem 8.1

description: MSP1 fragmented DNA

source_name: CD4+ memory t cell

tag: tissue

value: CD4+ memory t cell

tag: library prep kit

value: mRRBS

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate


title: RA5501B-4m: Treated Rheumatoid Arthritis patient CD4mem 1

description: MSP1 fragmented DNA

value: Diagenode mRRBS

value: Treated Rheumatoid Arthritis


title: lnN2D0A1  [BGISEQ-500]


title: Patient_40_E_Tm

tag: patient id

tag: gender

tag: age at diagnosis

tag: smoker

tag: drinker

tag: pathology report

tag: tumor size at maximum dimension

tag: rtx

value: N

tag: date of diagnosis

tag: date of 2nd recurrence

tag: date of 3rd recurrence


title: mTECs_from_Fezf2-3Flag_KI_mice_anti_Flag_ChIP_1

description:
ChIP_M2_Fezf2_1
processed data file: ATAC_WT.bw

tag: strain

tag: genotype/variation

tag: cell type

value: TECs

tag: chip antibody


title: IRC5103A-4N: Control CD4nai 3

description: MSP1 fragmented DNA

tag: tissue

value: CD4+ naïve t cell

tag: library prep kit

tag: disease state

value: Healthy control


title: lnN2D6  [BGISEQ-500]

tag: genotype

value: wild type

tag: age

value: day 6


title: SS1_2a

status: Public on Feb 06 2020

city: Providence

first: Emily

last: Petruccelli

state: Rhode Island

address: 185 Meeting Street

department: Neuroscience

institute: Brown University

description:
Flies treated 3x 10min ethanol, space 60min, sacrified 24hr later
transcript_count_matrix.csv

data_processing:
Trimmomatic (v.0.36): java -jar <path to jar file/trimmomatic-0.36.jar> SE <path to input> <path to output> ILLUMINACLIP:<TruSeq3-SE.fa>:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
HISAT2 (v.2.0.5): hisat2 -q -x <reference index/genome_tran> -U <input fastq file> -S <output sam file> -p 50
Samtools (v.1.3.1): samtools sort -@ 4 -o <output bam file> <input sam file>
StringTie (v.1.3.3): stringtie <input.sorted.bam> -b <path to Ballgown tables> -o <output.gtf> -G <reference.gtf>
prepDE.py: python <path to prepDE.py> -i <path to directory that contains all of the sample subdirectories>
Genome_build: BDGP6 + INTACT sequence
Supplementary_files_format_and_content: .csv

organism: Drosophila melanogaster

source_name: MB nuclei

growth_protocol: Flies raised at 25C, 65% humidity, light:dark 14hr:10hr

extract_protocol:
GFP immunoprecipitation, Trizol RNA extraction
Libraries prepared by GeneWiz (South Plainfield, NJ)

treatment_protocol: ~20,000 (for each biological replicate) 2-7 day old male MB010B>unc84-GFP (INTACT) flies collected under light CO2, allowed to recover O/N before treatment

tag: treatment

value: EtOH

tag: nuclei

value: MB010B > INTACT

tag: gender

value: male


title: SS1_2b


title: SS1_1c

description:
Flies treated 3x 10min air, space 60min, sacrified 24hr later
transcript_count_matrix.csv

value: Air


title: SS1_1a


title: SS1_2c


title: Patient_40_E_Nr

tag: batch

tag: patient id

value: M

tag: age at diagnosis

tag: smoker

value: current

tag: drinker

value: Y

tag: pathology report

value: Adjacent normal from anterior to posterior

tag: tumor size at maximum dimension

tag: Stage

tag: grade

value: moderate

value: left partial glossectomy

tag: qtx

tag: recurrence status

tag: date of 1st recurrence

tag: last follow-up

tag: date of death


title: SS1_1b

tag: treatment


title: f/f

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

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 Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped   to this gene.  FPKM, expected  number  of  Fragments  Per  Kilobase  of  transcript  sequence  per Millions  base  pairs  sequenced,  considers  the  effect  of  sequencing  depth  and  gene  length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010)
Genome_build: Ensemble_GRCm38.90
Supplementary_files_format_and_content: FPKM

source_name: BAT

extract_protocol:
iBATs were removed from BKO and f/f mice at 8 weeks old, flash frozen on liqid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: BAT

tag: age

value: 8 weeks

tag: genotype


title: BKO

value: METTL3flox/flox UCP1-iCre+/-


title: BKO_input

description: MeRIP-seq

data_processing:
The quality control of RAW data was used by fastqc (Version: v0.11.5).
Sequenced reads were trimmed for adaptor sequence by using skewer (Version: 0.1.126), and then mapped to Ensemble_GRCm38.90 whole genome using BWA (Version: 0.7.12-r1039) with parameters -T 25; -k 18.
Peaks were called using MACS2 (Version 2.1.0).
Motif search was detected by using homer findMotifGenome.pl (Version: v4.9.1) with parameters –gc; -len 8,10,12,14.
Genome_build: Ensemble_GRCm38.90

molecule: polyA RNA

source_name: brown adipose tissue

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany) from iBAT of Mettl3flox/flox and BKO mice .
Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Chemically fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation following the standard protocol of Magna MeRIPTM m6A Kit (MERK, 17-10499). Enrichment of m6A mRNA was then analyzed by high-throughput sequencing using Illumina Hiseq X platform.

treatment_protocol: Mettl3flox/flox and BKO mice were fed with normal chow diet for 8 weeks old

value: brown adipose tissue

tag: chip antibody

value: BKO (Mettl3 flox/flox UCP1-iCre)


title: Huvec_29_TNF

city: New York

first: Anne

middle: M

last: Bowcock

state: New York

address: One Gustave L. Levy Place, Box 1130

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Illumina hybridization protocol by Eurofins Genomics

scan_protocol: Illumina scanning protocol by Eurofins Genomics

data_processing: Gene expression data were processed with the limma R package. Outlier samples were detected with boxplots and classical multidimensional scaling (MDS) plots of the log2 probe intensities and removed from analysis. The neqc function was used to perform background correction and quantile normalization, log2 transformation of the probe intensities, and removal of control probes. Probes with expression detected (detection p<0.05) in less than half of the samples (n=28,386) were removed from analysis. The remaining 18,937 probes were collapsed to 14,019 genes by selecting the probe with the maximum mean intensity value for each gene using the collapseRows function. After quality control, 39 sample pairs (treated and untreated) remained for analysis.

source_name: Umbilical vein endothelial cells (primary cell line), treated with TNFa, 24 hours

label_protocol: Biotinylated cRNAs were generated by Eurofins Genomics

growth_protocol: Forty deidentified primary human umbilical vein endothelial cell (HUVEC) lines were obtained from Promocell and were cultured until passage four.

extract_protocol: RNA was isolated from cell pellets with Quiagen kits according to the protocol provided, and quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: Each cell line was split in half, and one half was treated with 20ng/mL TNFa for 24 hours while the other half was left untreated. Cells were then pelleted, and DNA and RNA were isolated.

value: treated with TNFa, 24 hours

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

value: newborn

tag: pedsex

tag: mds race

value: EUROPE

tag: cell type

value: Umbilical vein endothelial cells


title: Huvec_37_Untreated

source_name: Umbilical vein endothelial cells (primary cell line), untreated

value: untreated

value: male


title: Huvec_32_TNF


title: Huvec_38_TNF

value: female


title: Huvec_39_TNF


title: Huvec_36_Untreated


title: Huvec_30_Untreated


title: Huvec_32_Untreated


title: Huvec_36_TNF


title: Huvec_37_TNF


title: Huvec_29_Untreated


title: Huvec_33_TNF


title: Huvec_33_Untreated


title: Huvec_31_TNF


title: Huvec_30_TNF


title: Huvec_34_TNF


title: Huvec_39_Untreated


title: GS RA96h WCE H3K4me3 H3K27me3

city: Kyoto

first: Shinichiro

last: Chuma

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Institute for Frontier Life and Medical Sciences

institute: Kyoto university

data_processing:
ChIPseq reads were aligned to the mouse genome (mm10) using Bowtie2 2.3.4.1.
Macs2 2.1.0 callpeak and bdgcomp were used to process aligned ChIPseq reads.
Genome_build: mm10
Supplementary_files_format_and_content: Bdg files were generated by Macs2 2.1.0. Data represent fragment pileup per million reads subtracted by control lambda values.

source_name: GS RA96h

growth_protocol: Germline stem (GS) cells (kindly provided by Dr Takashi Shinohara) were cultured on mitomycin C treated primary embryonic fibroblast (PEF) cells according to the previous report (Kanatsu-Shinohara et al., Biol Reprod., 2003, 69, 612-616) with minor modifications. Before GS cell sampling, PEF cells were removed by a differential attachment method to gelatin coated dishes following standard procedures

extract_protocol:
For RAR ChIP, cells were fixed in 2 mM disuccinimidyl glutarate, 1.5 mM ethylene glycolbis succinimidyl succinate in PBS followed by 1% formaldehyde. Crosslinked cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris with protease inhibitors by sonication with Covaris S220. ChIP was performed by using anti-pan RAR antibody (Santa Cruz sc-773) and protein A/G agarose beads. For H3K4me3 and H3K27me3 ChIP, cells were fixed in 0.5% formaldehyde in PBS. Crosslinked cells were first lysed in 0.3M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 15 mM Tris, 0.5 mM DTT, 0.5% TritonX-100 with protease inhibitors, then nuclei were pelleted by centrifugation of the above lysates on 1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 15 mM Tris, 0.5 mM DTT. Nucleosome fractions were obtained by MNase treatment. ChIP was performed by using anti-H3K4me3 (Abcam ab8580) or anti-H3K27me3 (Upstate 07-449) and protein A/G agarose beads. For H3K27Ac ChIP, cells were fixed 1% formaldehyde in PBS. Crosslinked cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris with protease inhibitors by sonication with Covaris S220. ChIP was performed by using anti-H3K27Ac (Active motif 39133) and protein A/G agarose beads. Eluates were treated with RNase A and Proteinase K followed by phenol/chloroform extraction and ethanol precipitation of DNA.
For RAR, H3K4me3 and H3K27me3 ChIP, libraries were constructed from one (RAR) or five (H3K4me3 and H3K27me3) nanogram of ChIP DNA and five nanogram of input DNA using Illumina ChIP-seq sample prep kit (Illumina) and sequenced by GAIIX with Illumina Sequencing kit v4. For H3K27Ac ChIP-seq, libraries were constructed from one nanogram of ChIP DNA using TruSeq ChIP Sample Preparation Kit (Illumina) and sequenced by MiSeq with MiSeq Reagent Kit v2 (Illumina).

treatment_protocol: 100 nM retinoic acid (Sigma) was added to the culture media for times indicated in the file names. In order to suppress apoptosis in response to retinoic acid, BAX shRNA lentivirus vectors (GAGATGAACTGGACAGCAATA, TCAAGGCCCTGTGCACTAAAG) were transduced to GS cells or 50 uM Z-VAD-FMK was added to the culture media.

value: Germline stem (GS) cell line

tag: Sex

value: 100 nM retinoic acid for 96 hours

tag: antibody

value: anti-H3K4me3 (Abcam ab8580) and anti-H3K27me3 (Upstate 07-449)


title: Huvec_34_Untreated


title: Huvec_31_Untreated


title: flox_input

description: MeRIP-seq

value: Mettl3 flox/flox


title: Huvec_38_Untreated


title: flox_IP

description: MeRIP-seq

value: m6A antibody (Synaptic System, 202003)


title: Huvec_28_TNF


title: GS RA96h H3K27me3

value: anti-H3K27me3 (Upstate 07-449)


title: Huvec_28_Untreated


title: BKO_IP

description: MeRIP-seq


title: Huvec_27_TNF


title: GS RA96h H3K4me3

value: anti-H3K4me3 (Abcam ab8580)


title: GS control WCE H3K4me3 H3K27me3

source_name: GS control

value: Control


title: GS RA96h RAR

value: anti-pan RAR antibody (Santa Cruz sc-773)


title: GS control WCE RAR


title: GS control H3K27me3


title: GS control H3K4me3


title: GS control RAR


title: RNA-seq.2C-embryo_rep4

first: Jianlong

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: Embryo.gene.rep.matrix.tsv

data_processing:
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

source_name: 2C embryos

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 50 U/mL Penicillin/Streptomycin).

extract_protocol:
For ESCs, total RNAs were extracted using the RNeasy kit (#74136, Qiagen) according to the manufacturer’s instructions. For embryos, a total of 10-20 embryos with the same treatment and embryonic stage were pooled for each reaction. Injected embryos were harvested, washed several times in 0.5% BSA-PBS (Sigma) solution and subsequently picked and transferred into lysis buffer by a mouth pipette.
For ESCs, 1 µg total RNA from each sample was taken for the preparation of PolyA RNA-seq libraries, and massively parallel sequencing was performed with the HiSeq4000 platform. Paired-end 150 bp-length reads were produced. For embryos, RNA-seq libraries were prepared according to the Smart-seq2 protocol (Picelli et al., 2014) with minor modifications. After reverse transcription, cDNA was pre-amplified (10 PCR cycles) and purified with Ampure XP Beads (Agencourt) at 0.8 beads/1 DNA (v/v). One microliter (1 μl) cDNA, dulited by 19 μl nuclease-free water, was used for Real-time PCR quality check. The amplified cDNA was fragmented using a Covaris sonicator (Covaris S220). To generate the sequence libraries, the KAPA Hyper Prep Kit was used following the manufacturer’s instructions. NOVA pair-end 150-bp sequencing was performed on a HiSeq 2500 sequencer (Illumina) at Berry Genomics Corporation.

treatment_protocol: B6D2F1 (BDF1) female mice (7-8 weeks old) were superovulated by intraperitoneally injecting with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (hCG), and then mated to BDF1 male mice. The fertilized embryos (zygotes) were collected from oviducts. A mixture of Zmym2 siRNA (20 µM), scramble siRNA (20 µM), miRNA (50 µM), or scramble miRNA (50 µM) was separately injected into the cytoplasm of fertilized eggs with visible pronuclei. The injected zygotes were then cultured in G1 plus medium (10128, Vitrolife), and 2-cell, 4-cell, 8-cell, morula and blastocyst embryos were obtained after culturing.

value: Mouse embryos

value: Whole embryo

value: B6D2F1 (BDF1)


title: RNA-seq.2C-embryo_rep2

description: Embryo.gene.rep.matrix.tsv


title: RNA-seq.2C-embryo_rep1

description: Embryo.gene.rep.matrix.tsv


title: Eric_S5

city: Los Angeles

first: Nathan

last: Lubock

email: nlubock@ucla.edu, nate@octant.bio

state: CA

address: 607 Charles E Young Drive

institute: UCLA

data_processing:
For NextSeq_MiSeq.map.csv.gz - We used the BBTools suite(https://jgi.doe.gov/data-and-tools/bbtools/) of programs to  process our sequencing data using the default settings unless otherwise noted. First,  we used BBDuk2 to filter out any reads matching PhiX (k=23, mink=11, hdist=1) and to  trim off any Illumina sequencing adapters. We then used BBMerge to merge our paired  end reads. We performed another round of trimming with BBDuk2 to ensure no  adapters were left over after merging and to remove any sequence with an N base call.  After merging and trimming the reads, we used a custom Python script (bcmap.py) to  generate a consensus nucleotide sequence for each barcode.  Briefly the script works as follows. First, we split each read into the 15 nt barcode and its  corresponding variant. We then generate a dictionary that maps each barcode to its list  of unique sequences and their counts. To enable majority basecalls, we drop any  barcode that has less than 3 reads. We then pass the barcodes through a series of  filters to eliminate potential errors introduced by barcodes that are mapped to multiple  variants. Since we barcoded and mutagenized the ADRB2 gene in separate pieces,  barcodes can be contaminated with variants from different parts of the ADRB2 gene.  We address this case by using BBMap to align every barcode’s sequences to the  ADRB2 reference and consider that barcode to be contaminated if any sequence aligns  >5 nt away from the most common sequence. Another source of contamination comes  from the chip-synthesized library itself, which contains a significant number of single  base deletions. We consider a barcode contaminated if it has any sequences of  different lengths as it is unlikely that a single base deletion will come from an Illumina  sequencer by chance. However, these filters would not catch the case where a barcode  is contaminated with variants from the same piece of ADRB2. As we only synthesized  the missense variants, we expect variants within the same piece of ADRB2 to be a  Levenshtein distance of 4 from each other on average (approximately two changes to  WT and two changes to a new codon). Thus, we drop any barcode that has a sequence  with >1 read at a Levenshtein distance of 4 away from that barcode’s most common  sequence. Lastly, we generate a consensus sequence by taking the majority base call  at each position and call an N at any ties.
For drug-*_cond-bcs-counts.txt.gz we used awk to substring and count the first 15 nt, which corresponds to the barcode. We then join in addional information such as the drug condition and repeat.

molecule: other

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: Cells were HEK293T derived and grown in DMEM+10%FBS+PS

extract_protocol:
Qiagen Plasmid Plus Maxi Kit
Determining ADRB2 variant-barcode associations. After barcoding variants, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
Cells were lysed (buffer supplied in the kit) on the dishes and prepped according to the manufacturer's protocol (RNeasy miniprep)
The plasmid DNA library construction is simple Illumina amplicon sequencing.
RNA was reverse transcribed (Superscript IV) with a gene specific primer and the resulting cDNA was amplified with primers containing necessary adaptors for illumina sequencing

treatment_protocol: Media was replaced with OptiMEM and treated with vehicle, isoproterenol (ADRB2 agonist), or forskolin (cAMP stimulant)

tag: growth medium

value: LB

tag: molecule

value: Plasmid DNA


title: AT Pre 20275 [US.1581538]

city: Seattle

first: Sara

middle: A

last: Murray

state: WA

address: 530 Fairview Ave N

department: Obesity Research Group

institute: Novo Nordisk Research Center Seattle, Inc.

description:
sample name:
US.1581538

data_processing:
Sequenced library and read quality was assessed using fastqc.
Sequenced reads were aligned using STAR to the MacaM reference genome. Macaque genes were matched to the closest human homolog, defined as the gene with a symbol that matched the macaque symbol and had a canonical Uniprot entry.
Library quality: samples that had at least 75% of reads uniquely mapped to the genome and at least 10 million total reads were included in the analysis.
Gene filtering: genes that had log2 counts per million of at least 1 in one quarter of libraries were included in the analysis.
Normalization: gene expression counts were normalized within each tissue type using edgeR calcNormFactors to produce the gene_count_matrix processed data table.  Counts were further normalized using limma voomWithQualityWeights during differential gene expression analysis.
Sample identity was confirmed by two methods. First, by comparing the expression levels of genes known to be highly expressed in, or specific to, adipose tissue and skeletal muscle (Human Protein Atlas).  Second, by comparing SNP variants between sample libraries that came from the same animal: a list of SNPs was compiled from the indexed BAM files of all samples using samtools mpileup and filtered to high confidence, highly expressed SNPs using bcftools filter.  Samples were compared using BAM-matcher with the Varscan option.  Samples with a fraction of SNPs in common above 90% were from the same animal, whereas samples from different animals had a fraction in common of below 80%.
Genome_build: MacaM Rhesus macaque genome
Supplementary_files_format_and_content: gene_count_matrix.csv, where rows are genes/features and columns are samples.  Values are TMM normalized counts (not log2 or cpm transformed). Four samples that did not pass library QC are not included.

organism: Macaca mulatta

source_name: Subcutaneous adipose tissue

extract_protocol:
Tissue punch biopsies were taken from adipose and skeletal muscle tissue, snap frozen in liquid nitrogen, and stored at -80 degrees.  Samples were then thawed and homogenized in Trizol using a TissueLyser II (Qiagen).  RNA was extracted using chloroform and a Qiagen RNeasy Mini Kit following the manufacturer's instructions.
cDNA libraries were constructed with Illumina TruSeq stranded mRNA kit and sequenced on an Illumina HiSeq2000 using paired-end, 50 nucleotide reads.

value: Subcutaneous adipose tissue

tag: animal

value: Pre


title: Huvec_26_Untreated

tag: treatment

value: untreated

value: newborn

value: female

value: EUROPE

value: Umbilical vein endothelial cells


title: AT Pre 26292 [US.1581535]

description:
sample name:
US.1581535


title: Huvec_25_Untreated


title: CCT3 KD-3

city: NanJing

first: Feng

last: Zhang

state: JiangSu

address: Weigang NO.1

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

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

source_name: A-375 infected with CCT3 knockdown lentivirus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: A-375 cell line was cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37 °C in a humidified incubator with 5% CO2.

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

treatment_protocol: A-375 cells infected with NC lentivirus or CCT3 knockdown lentivirus for 16 hours before media were exchanged with fresh media. Then cells were cultured for 72 hours before cells were harvested and prepared for RNA extration and genechip analysis.

tag: cell line

value: human melonoma cell line

tag: genotype/variation

value: CCT3 knockdown


title: CCT3 KD-2


title: Huvec_25_TNF

value: treated with TNFa, 24 hours


title: RNA-seq.2C-embryo_rep3

description: Embryo.gene.rep.matrix.tsv

tag: tissue

tag: strain


title: LysMCre-Cripto-deficient macrophages Rep 1

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed by means of a pipeline that used FastQC, to asses read quality, and Cutadapt 1.7.1 to trim sequencing reads, eliminating Illumina adaptor remains, and to discard reads that were shorter than 30 bp.
The resulting reads were mapped against the mouse transcriptome (GRCm38, release 91; dec2017 archive) and quantified using RSEM v1.2.20.
Data were normalized using Voom with the Bioconductor package EdgeR-limma
Genome_build: GRCm38, release 91
Supplementary_files_format_and_content: tab-delimited text files include Voom-normalized counts per million reads sequenced

source_name: Skeletal muscle macrophage

extract_protocol:
To induce muscle damage, cardiotoxin was injected in the tibialis anterior, gastrocnemius and quadriceps muscles for 5 days. Muscles were removed and separated from the bones, and dissociated by enzymatic digestion using 3U/mL Dispase II, 0.5U/mL Collagenase A, 10μg/mL DNAse I , 400μM CaCl2 and 5μM MgCl2 in PBS, for 75 minutes in a shaking bath at 37 °C. Cells were then washed with DMEM and filtered with 100 µm and 70 µm cell strainers. Following filtration, red blood cells were removed, and the remaining cells were re-suspended in PBS 2% FBS (FACS buffer). Macrophages were blocked using purified Rat Anti-Mouse CD16/CD32 (Mouse BD Fc Block™; 1:100) for 15 minutes at 4 °C and then incubated with the indicated primary antibodies for 30 minutes at 4 °C. After washing with ice-cold PBS, cells were either analysed or sorted with a FACSAria II (BD Biosciences.  RNA was harvested using the combination of QIAzol Lysis Reagent and RNAeasy minikit columns (Qiagen) following the manufacturer’s instructions.
cDNA library preparation and amplification were performed from 200 ng total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina.

value: Skeletal muscle

value: Macrophages

tag: age

value: 3 months

tag: genotype

value: male


title: Huvec_27_Untreated

tag: promocell catalogue number

tag: promocell lot number


title: LysMCre-Cripto-deficient macrophages Rep 2


title: WT macrophages Rep 3

value: wild type


title: NC-2

source_name: A-375 infected with NC lentivirus

value: control


title: NC-1


title: NC-3


title: CCT3 KD-1


title: WT macrophages Rep 2


title: Huvec_26_TNF

tag: promocell age

tag: pedsex


title: WT macrophages Rep 1

tag: cell type


title: Huvec_24_TNF

tag: mds race


title: Huvec_24_Untreated


title: LysMCre-Cripto-deficient macrophages Rep 3

tag: Sex


title: RNA-seq.NC_injection_blastocyst

description:
Embryo.gene.rep.matrix.tsv
Mouse embryos

source_name: Embryos with zygote injection of non-targeting control RNA, RNA collected at blastocyst stage

value: Whole embryo

value: B6D2F1 (BDF1)

value: non-targeting control RNA


title: Gastroc Wash 21189 [US.1581526]

description:
sample name:
US.1581526

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle

value: Wash


title: Huvec_23_Untreated

value: untreated

value: newborn


title: Gastroc Wash 22130 [US.1581524]

description:
sample name:
US.1581524


title: Huvec_23_TNF

value: EUROPE

value: Umbilical vein endothelial cells


title: RNA-seq.NC_injection_8cell

source_name: Embryos with zygote injection of non-targeting control RNA, RNA collected at 8-cell stage


title: AT Wash 23004 [US.1581517]

description:
sample name:
US.1581517

value: Subcutaneous adipose tissue


title: RNA-seq.siZmym2_arrested_1

source_name: Embryos with zygote injection of Zmym2 siRNA, with arrested developmental morphology, RNA collected at 8-cell/early morula stage

value: Zmym2 siRNA


title: RNA-seq.miR344_mimics_normal_blastocyst

source_name: Embryos with zygote injection of miR-344 mimics RNA, with normal developmental morphology, RNA collected at blastocyst stage

value: miR-344 mimics


title: RNA-seq.miR344_mimics_normal_8cell_1

source_name: Embryos with zygote injection of miR-344 mimics RNA, with normal developmental morphology, RNA collected at 8-cell stage


title: RNA-seq.miR344_mimics_normal_8cell_0


title: RNA-seq.siZmym2_arrested_0


title: AT Wash 20261 [US.1581514]

description:
sample name:
US.1581514


title: ATAC-seq.DR+/+_rep2

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to mouse genome (NCBI build 37, mm9) using the bowtie2 (v2.3.0) program, with parameters -X 2000 --no-mixed.
Aligned reads were filtered by samtools (v0.1.19) program with parameters -F 0x04 -f 0x02 -q 20.
ATAC-seq peaks were determined by the MACS program (v.2.0.10) with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of MACS called peaks.

source_name: Embryonic stem cells

extract_protocol:
ATAC-seq libraries of mESCs were prepared as previously described (Buenrostro et al., 2015) with minor modifications. Briefly, samples were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.15% NP-40) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spin down, incubated with the Tn5 transposase and tagmentation buffer at 37 °C for 30 min.
ATAC-seq library was prepared following a protocol (Buenrostro et al., 2013), and sequenced by Illumina HiSeq2500 at New York University Genome Technology Center following a standard protocol. Paired-end 50bp-length ATAC reads were produced.

value: mESC J1

tag: mouse strain

tag: cell population

value: DR+/+ (MERVL+/Zscan4c+) population


title: AT Post 22130 [US.1581513]

description:
sample name:
US.1581513

tag: animal

value: Post


title: RNA-seq.siZmym2_normal_8cell_1

source_name: Embryos with zygote injection of Zmym2 siRNA, with normal developmental morphology, RNA collected at 8-cell stage


title: ATAC-seq.DR+/+_rep1


title: RNA-seq.siZmym2_normal_8cell_0


title: ATAC-seq.DR-/-_rep2

value: DR-/- (MERVL-/Zscan4c-) population


title: Gastroc Wash 20275 [US.1581509]

description:
sample name:
US.1581509


title: Gastroc Post 21866 [US.1581508]

description:
sample name:
US.1581508


title: Huvec_22_TNF

source_name: Umbilical vein endothelial cells (primary cell line), treated with TNFa, 24 hours

tag: treatment

value: treated with TNFa, 24 hours

value: female


title: GS_control_IgG_crosslink3

description: control IgG ChIP

data_processing:
ChIPseq reads were aligned to the mouse genome (mm10) using Bowtie2 2.3.4.1.
Macs2 2.1.0 callpeak and bedGraphcomp were used to process aligned ChIPseq reads.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated by Macs2 2.1.0. Data represent fold enrichment scores relative to control lambda values.

extract_protocol:
For crosslink1, cells were fixed in 2 mM disuccinimidyl glutarate, 1.5 mM ethylene glycolbis succinimidyl succinate in PBS followed by 1% formaldehyde. Crosslinked cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris with protease inhibitors by sonication with Covaris S220. ChIP was performed by using normal rabbit IgG (Upstate 12-370) and protein A/G agarose beads. For crosslink2, cells were fixed in 0.5% formaldehyde in PBS. Crosslinked cells were first lysed in 0.3M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 15 mM Tris, 0.5 mM DTT, 0.5% TritonX-100 with protease inhibitors, then nuclei were pelleted by centrifugation of the above lysates on 1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 15 mM Tris, 0.5 mM DTT. Nucleosome fractions were obtained by MNase treatment. ChIP was performed by using normal rabbit IgG (Upstate 12-370) and protein A/G agarose beads. For crosslink3, cells were fixed in 1% formaldehyde in PBS. Crosslinked cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris with protease inhibitors by sonication with Covaris S220. ChIP was performed by using normal rabbit IgG (Upstate 12-370) and protein A/G agarose beads. Eluates were treated with RNase A and Proteinase K followed by phenol/chloroform extraction and ethanol precipitation of DNA.
Libraries were constructed from control IgG ChIP DNA or genomic DNA (from whole cell extract) using TruSeq ChIP Sample Preparation Kit (Illumina) and sequenced by MiSeq with MiSeq Reagent Kit v3 (Illumina).

value: Germline stem (GS) cell line

value: male

value: control

tag: antibody

value: normal rabbit IgG (Upstate 12-370)


title: GS_control_WCE_crosslink3

description: genomic DNA from whole cell extract


title: AT Pre 21866 [US.1581507]

description:
sample name:
US.1581507

value: Pre


title: RNA-seq.siZmym2_normal_blastocyst

source_name: Embryos with zygote injection of Zmym2 siRNA, with normal developmental morphology, RNA collected at blastocyst stage

value: Whole embryo

value: B6D2F1 (BDF1)

tag: genotype/variation


title: Gastroc Post 24849 [US.1581521]

description:
sample name:
US.1581521

tag: tissue

value: Gastrocnemius muscle


title: AT Post 21189 [US.1581506]

description:
sample name:
US.1581506

value: Subcutaneous adipose tissue


title: Huvec_21_Untreated

source_name: Umbilical vein endothelial cells (primary cell line), untreated

value: untreated

value: newborn

value: EUROPE

value: Umbilical vein endothelial cells


title: GS_control_IgG_crosslink2

description: control IgG ChIP


title: GS_control_IgG_crosslink1

description: control IgG ChIP


title: Huvec_22_Untreated


title: Huvec_20_TNF


title: ATAC-seq.DR-/-_rep1

tag: cell line

value: mESC J1


title: Huvec_20_Untreated


title: Huvec_19_Untreated


title: Huvec_19_TNF


title: GS RA120h H3K27Ac

source_name: GS RA120h

value: 100 nM retinoic acid for 120 hours

value: anti-H3K27Ac (Active motif 39133)


title: GS control H3K27Ac

source_name: GS control

value: Control


title: PEF control RNA

data_processing:
RNA-seq reads were aligned to the mouse genome (mm10) using Hisat2 2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKM) were calculated by Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Text files including FPKM values calculated by Cufflinks 2.2.1.

source_name: PEF control

growth_protocol: Germline stem (GS) cells (kindly provided by Dr Takashi Shinohara) were cultured on mitomycin C treated primary embryonic fibroblast (PEF) cells according to the previous report (Kanatsu-Shinohara et al., Biol Reprod., 2003, 69, 612-616) with minor modifications. Before GS cell sampling, PEF cells were removed by a differential attachment method to gelatin coated dishes following standard procedures. Embryonic stem (ES) cells (kindly provided by Dr Junichi Takeda) were grown in feeder-free naive state (2iLIF) conditions according to the previous report (Ying et al., Nature, 2008, 453, 519-523) with minor modifications. Primary embryonic fibroblast (PEF) cells were prepared from mouse embryos according to standard procedures and used for experiments at three to five passages .

extract_protocol:
Total RNAs were extracted with Trizol reagent (Invitrogen) according to the manufacturer's instructions. Agilent 2100 bioanalyzer was used to assess the quality of total RNAs (RIN > 8).
Libraries were constructed from one microgram of total RNA using TruSeq RNA Sample Preparation Kit v2 (illumina) and sequenced by MiSeq with MiSeq Reagent Kit v2 (Illumina) .

treatment_protocol: 100 nM retinoic acid was added to the culture media for times indicated in the file names. BAX shRNA lentivirus vectors (GAGATGAACTGGACAGCAATA, TCAAGGCCCTGTGCACTAAAG) were transduced to GS cells in order to suppress apoptosis in response to retinoic acid.

value: male and female


title: AT Pre 21189 [US.1581505]

description:
sample name:
US.1581505

source_name: Subcutaneous adipose tissue


title: Gastroc Pre 19832 [US.1581504]

description:
sample name:
US.1581504


title: ES RA120h RNA

source_name: ES RA120h

value: Embryonic stem (ES) cell line

value: male


title: AT Post 20275 [US.1581502]

description:
sample name:
US.1581502

value: Post


title: GS RA120h RNA

value: Germline stem (GS) cell line


title: AT Post 20261 [US.1581499]

description:
sample name:
US.1581499


title: Huvec_18_Untreated


title: Huvec_18_TNF

value: treated with TNFa, 24 hours


title: Huvec_17_TNF

value: female


title: GS RA72h RNA

source_name: GS RA72h

value: 100 nM retinoic acid for 72 hours


title: Huvec_17_Untreated


title: pullout_miR-28_bio_replicate_1

city: Copenhagen

first: Francesco

last: Russo

address: Blegdamsvej 3b

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

data_processing:
NGS data were analysed using the Galaxy platform (https://usegalaxy.org/)
Quality control step: FastQC (version 0.10.1)
Trimming: Cutadapt
Aligner: TopHat 2 (version 2.0.9)
Transcript assembly and FPKM estimation: Cufflinks (version 2.1.1)
Merging of Cufflinks assemblies: Cuffmerge
Finding significant changes in transcript expression: Cuffdiff
Genome_build: Human genome hg38
Supplementary_files_format_and_content: Tab separated files reporting the Cufflinks output (FPKM)

source_name: prostate cancer cell line

growth_protocol: DU-145 cell lines grew in RPMI Medium 1640 (EuroClone). The medium was completed by adding 10% FBS (Fetal Bovine Serum, EuroClone), 1% penicillin (10.000 U/ml) and 1% streptomycin (10.000 mg/ml) (EuroClone) and 1% L-glutamine (200mM, Sigma-Aldrich). The cells were grew at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted adding directly on adherent cells TRIzol reagent (Thermo Fisher) and following the instructions provided by the manufacturer. After DNAse treatment, 15 μg of RNA was incubated for 4 hrs at 4°C with 100 μl of streptavidin-conjugated beads (200 μl of Streptavidin Sepharose high performance, GE Healthcare) previously suspended in PO buffer (1M Tris pH8, 5M NaCl, 1M MgCl2, NP40 50 μl in 100 ml buffer). After 2 washes with PO buffer and 2 washes with DEPC-treated water, the RNA complexed with beads was recovered by adding 1 ml Trizol directly on the beads and then following the TRIzol RNA extraction protocol.
The RNA isolated after the miRNA pullout procedure from both miR-28CT and miR-28BIO samples was used for the construction of the cDNA libraries using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina) according to the manufacturer’s suggestions. cDNA libraries were sequenced by HiSeq2000 (Illumina) in single-reads mode (50bp) by IGA Technology Service, Udine, Italy, obtaining about 20 million of reads for each samples.

treatment_protocol: DU-145 cell lines were seeded into the wells of a 6-well at the density of 1.5 x105. After 24 hours from seeding, cells were transfected using lipofectamine (Thermo Fisher) with 60nM of either miR-28-5p duplex (ds-miR-28CT) or a mix of 3’ biotin-tagged miR-28-5p 8tU (nucleotide 8 was a thiouridine) and miR-28-5p 18tU duplexes (ds-miR-28BIO). The day after transfection, the cells were washed with PBS and irradiated with UV (365nm, 2J/cm2), using the Bio-Link crosslinking (BLX) (Ambrose Lourmat) with appropriate UV lamps, to induce cross-linking of tU nucleotides to RNA.

tag: transfection

value: cells were transfected using lipofectamine (Thermo Fisher) with 60nM of  a mix of 3’ biotin-tagged miR-28 8tU (nucleotide 8 was a thiouridine) and miR-28-5p 18tU duplexes (ds-miR-28BIO)


title: AT Post 24849 [US.1581497]

description:
sample name:
US.1581497

value: Subcutaneous adipose tissue


title: Huvec_16_TNF

value: newborn


title: GS control RNA


title: pullout_miR-28_control_replicate_1

value: cells were transfected using lipofectamine (Thermo Fisher) with 60nM of miR-28-5p duplex (ds-miR-28CT)


title: pullout_miR-28_bio_replicate_2

value: cells were transfected using lipofectamine (Thermo Fisher) with 60nM of  a mix of 3’ biotin-tagged miR-28-5p 8tU (nucleotide 8 was a thiouridine) and miR-28-5p 18tU duplexes (ds-miR-28BIO)


title: Gastroc Wash 24849 [US.1581496]

description:
sample name:
US.1581496

source_name: Gastrocnemius muscle

value: Gastrocnemius muscle

value: Wash


title: ES control RNA

source_name: ES control


title: Gastroc Post 21189 [US.1581494]

description:
sample name:
US.1581494


title: Huvec_21_TNF

value: EUROPE

value: Umbilical vein endothelial cells


title: pullout_miR-28_control_replicate_2


title: GS RA24h RNA

source_name: GS RA24h

value: 100 nM retinoic acid for 24 hours


title: Gastroc Wash 21866 [US.1581489]

description:
sample name:
US.1581489


title: AT Pre 20261 [US.1581493]

description:
sample name:
US.1581493

value: Pre


title: Huvec_16_Untreated

value: untreated


title: AT Pre 24849 [US.1581487]

description:
sample name:
US.1581487


title: Huvec_14_TNF


title: Apocrine glands of lesional skin-female 8

city: Dessau

first: Christos

middle: C

last: Zouboulis

address: Auenweg 38

department: Departments of Dermatology, Venereology, Allergology and Immunology

country: Germany

institute: Dessau Medical Center, Brandenburg Medical School Theodor Fontane

hyb_protocol: RNA fragmentation was performed by incubation with 10x GEX Blocking Agent and Fragmentation Buffer (Agilent) for 30 minutes at 60°C. Then, 2x GEX hybridization buffer (Agilent) was added and samples were loaded on array slides. Hybridization was performed at 65°C at 10 rpm for 17 h and then washed with GEX wash buffer 2 (Agilent).

scan_protocol: Arrays were scanned using the Agilent Scanner.

data_processing:
Images were processed using the Agilent Feature Extraction software to generate text files.
Raw transcriptome profile data were preprocessed using the limma package in R. Background correction was performed using the normexp convolution model and corrected data were subsequently normalized using Loess normalization. After preprocessing, the control and low intensity probe sets were filtered out to improve the signal of further analyses. Low intensity probe sets were defined as those with an intensity less than 10% brighter than the 95th percentile of the negative control probe sets in at least eight arrays. Ratios were computed using the RosettaResolver™ Software (Rosetta Inpharmatics, Seattle, WA, USA). The significant genes were investigated using Enrichr.

source_name: skin

label_protocol: The Low Input Quick Amp Labeling Kit, one-color (Agilent) including the dye cyanine 3-labeled CTP (Cy3-CTP) was used.

extract_protocol: RNA isolation from the homogenates was performed using the RNeasy® Mini Kit (Qiagen) including DNase I on column treatment following the manufacturer's protocol.

value: apocrine glands

tag: age


title: Huvec_15_TNF

tag: promocell catalogue number


title: Huvec_14_Untreated

tag: promocell lot number


title: Huvec_15_Untreated

tag: promocell age


title: Huvec_13_TNF

tag: pedsex


title: AT Pre 19832 [US.1581478]

description:
sample name:
US.1581478


title: Apocrine glands of lesional skin-female 5


title: Apocrine glands of lesional skin-female 2


title: GS RA96h WCE RAR

source_name: GS RA96h

tag: cell type

value: Germline stem (GS) cell line

value: male

value: 100 nM retinoic acid for 96 hours

value: anti-pan RAR antibody (Santa Cruz sc-773)


title: Apocrine glands of lesional skin-female 1


title: Apocrine glands of lesional skin-female 6


title: Apocrine glands of lesional skin-female 4


title: Apocrine glands of lesional skin-female 7


title: Gastroc Wash 23004 [US.1581492]

description:
sample name:
US.1581492


title: Gastroc Pre 21866 [US.1581477]

description:
sample name:
US.1581477


title: Huvec_12_TNF

value: treated with TNFa, 24 hours

tag: mds race


title: Huvec_13_Untreated

value: female


title: AT Post 26292 [US.1581476]

description:
sample name:
US.1581476

value: Subcutaneous adipose tissue

value: Post


title: Apocrine glands of lesional skin-male 8


title: AT Wash 21189 [US.1581475]

description:
sample name:
US.1581475


title: Gastroc Wash 19832 [US.1581473]

description:
sample name:
US.1581473


title: Apocrine glands of lesional skin-male 6


title: Apocrine glands of lesional skin-female 3


title: Gastroc Pre 20275 [US.1581472]

description:
sample name:
US.1581472


title: Huvec_11_TNF

value: newborn


title: AT Wash 21866 [US.1581471]

description:
sample name:
US.1581471


title: Apocrine glands of lesional skin-male 4


title: Apocrine glands of lesional skin-male 5


title: Huvec_12_Untreated


title: Apocrine glands of lesional skin-male 3


title: Apocrine glands of non-involved skin-female 8


title: Huvec_9_TNF


title: AT Post 21866 [US.1581466]

description:
sample name:
US.1581466


title: Apocrine glands of non-involved skin-female 2


title: Apocrine glands of lesional skin-male 1


title: Apocrine glands of non-involved skin-female 7


title: Apocrine glands of non-involved skin-male 8


title: Apocrine glands of non-involved skin-female 4


title: Apocrine glands of lesional skin-male 2


title: Huvec_10_Untreated


title: Apocrine glands of non-involved skin-female 3


title: Huvec_10_TNF


title: Apocrine glands of non-involved skin-female 5


title: Apocrine glands of non-involved skin-female 6


title: Apocrine glands of non-involved skin-male 7


title: AT Wash 22130 [US.1580325]

description:
sample name:
US.1580325


title: Huvec_8_TNF


title: Gastroc Pre 23004 [US.1580319]

description:
sample name:
US.1580319

value: Gastrocnemius muscle


title: AT Pre 20456 [US.1580315]

description:
sample name:
US.1580315


title: AT Pre 22130 [US.1580311]

description:
sample name:
US.1580311


title: LungEC-R2

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description: FACS sorted cells

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the 6pb index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M13, based on Ensembl version 88
Expression values were also computed using RSEM version 1.2.28 based on Gencode M13 transcript annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: lung EC from C57BL/6J mice

extract_protocol:
KAPA RNA HyperPrep PolyA
TriZol + RNeasy mini Kit (Qiagen, #74106)

tag: strain

value: 8 weeks

tag: Sex

value: Male

value: primary lung epithelial cells

value: Lung


title: LungEC-R3

description: FACS sorted cells


title: Apocrine glands of non-involved skin-female 1


title: ColonEC-R2

description: FACS sorted cells

source_name: colon EC from C57BL/6J mice

value: primary colon epithelial cells

value: Colon


title: AT Post 23004 [US.1580308]

description:
sample name:
US.1580308


title: ColonEC-R3

description: FACS sorted cells


title: ColonEC-R1

description: FACS sorted cells


title: Huvec_8_Untreated

value: untreated

value: EUROPE

value: Umbilical vein endothelial cells


title: Huvec_7_Untreated

value: male


title: Huvec_7_TNF

source_name: Umbilical vein endothelial cells (primary cell line), treated with TNFa, 24 hours


title: Apocrine glands of non-involved skin-male 2

value: apocrine glands


title: Apocrine glands of non-involved skin-male 6


title: Apocrine glands of non-involved skin-male 5


title: AT Wash 20275 [US.1580304]

description:
sample name:
US.1580304

value: Wash


title: Skin_R3

description: FACS sorted cells

source_name: skin EC from C57BL/6J mice

extract_protocol:
KAPA RNA Stranded PolyA
TriZol + RNeasy mini Kit (Qiagen, #74106)

value: primary skin epithelial cells

value: Skin


title: Apocrine glands of non-involved skin-male 1


title: Huvec_6_TNF

value: treated with TNFa, 24 hours

value: female


title: Skin_R1

description: FACS sorted cells


title: AT Pre 23004 [US.1580286]

description:
sample name:
US.1580286

value: Subcutaneous adipose tissue

value: Pre


title: LungEC-R1

description: FACS sorted cells

value: 8 weeks

value: Male


title: mTEC_R3

description: FACS sorted cells

source_name: mTEC from C57BL/6J mice

value: primary medullary thymic epithelial cells

value: Thymus


title: mTEC_R2

description: FACS sorted cells


title: Gastroc Pre 20456 [US.1580283]

description:
sample name:
US.1580283

value: Gastrocnemius muscle


title: Huvec_11_Untreated

source_name: Umbilical vein endothelial cells (primary cell line), untreated

value: untreated

value: newborn


title: mTEC_R1

description: FACS sorted cells


title: Skin_R2

description: FACS sorted cells


title: AT Wash 24849 [US.1580279]

description:
sample name:
US.1580279


title: cTEC_R3

description: FACS sorted cells

source_name: cTEC from C57BL/6J mice

value: primary cortical thymic epithelial cells


title: Huvec_5_TNF

value: EUROPE

value: Umbilical vein endothelial cells


title: Huvec_6_Untreated


title: cTEC_R2

description: FACS sorted cells


title: Huvec_5_Untreated


title: Gastroc Wash 20456 [US.1580277]

description:
sample name:
US.1580277

value: Wash


title: cTEC_R1

description: FACS sorted cells


title: AT Post 20456 [US.1580266]

description:
sample name:
US.1580266

value: Post


title: siZFC3H1_xPAP_ip_batch4

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

institute: Aarhus University

data_processing:
3'end seq reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
The data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from bam files using a custom script. The score represents normalized counts per base.

source_name: tissue culture cells

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNAs were extracted using TRIzol (Invitrogen) according to the manufacturer’s protocol and then treated with TURBO DNase (Invitrogen) following the manufacturer’s instruction to remove contaminating genomic DNA. Six in vitro transcribed spike-in RNAs were added. Sequences for spike-ins are identical to ERCC spike-ins. ERCC-00092, ERCC-00136 and ERCC-00043 were transcribed in the presence of 4sU, whereas ERCC-00170, ERCC-00002 and ERCC-00145 were transcribed without 4sU and serve as negative control in the 4sU purification step.
An aliquot of  each RNA was analyzed as total RNA, spiked with an additional full complement of commercially available ERCC spike-ins. The remainder of RNA was used for 4sU purification. Half of all total and 4sU labelled RNA samples were 3'end polydenylated in vitro using E.coli poly(A) polymerase ('xPAP'). All samples were rRNA depleted and subjected to pA+ RNA 3'end sequencing using QuantSeq REV kit from Lexogen GmbH. 8 or 10 libraries were multiplexed and sequenced at the Vienna Biocenter Core Facilities with a NextSeq SR75 High Output run.
RNA 3'end seq, single-end

treatment_protocol: siRNA transfections were performed targeting EGFP(control), RBM7, RRP40,  ZCCHC8, ZFC3H1 or ZCCHC8+ZFC3H1. Cells were transfected with siRNAs twice with the second time repeated after two days, and then cell were cultured for another two days. 10 min before harvesting, 4-thiouridine (4sU) was added to the growth medium for metabolic labelling of early RNA.

value: HeLa

tag: sirna

tag: rna fraction

value: xPAP

tag: pap treatment

value: ip

tag: batch


title: siZFC3H1_xPAP_ip_batch3


title: Gastroc Pre 22130 [US.1577093]

description:
sample name:
US.1577093

tag: animal


title: siZFC3H1_xPAP_in_batch1

value: in


title: Huvec_3_TNF

tag: treatment

value: treated with TNFa, 24 hours

value: male


title: siZFC3H1_xPAP_in_batch3

tag: cell line


title: siZFC3H1_xPAP_in_batch2


title: siZFC3H1_noPAP_ip_batch4

value: noPAP


title: Gastroc Post 20275 [US.1577087]

description:
sample name:
US.1577087

tag: tissue


title: Huvec_3_Untreated


title: Gastroc Post 20456 [US.1577086]

description:
sample name:
US.1577086


title: siZFC3H1_noPAP_in_batch3


title: siZFC3H1_noPAP_ip_batch3


title: Gastroc Pre 24849 [US.1577083]

description:
sample name:
US.1577083

value: Pre


title: siZFC3H1_noPAP_in_batch1


title: siZFC3H1_noPAP_in_batch2


title: Huvec_4_TNF

value: female


title: Huvec_2_TNF


title: siZCCHC8+ZFC3H1_xPAP_ip_batch4


title: siZCCHC8+ZFC3H1_xPAP_ip_batch3


title: AT Wash 26292 [US.1577073]

description:
sample name:
US.1577073

source_name: Subcutaneous adipose tissue

value: Subcutaneous adipose tissue


title: siZCCHC8+ZFC3H1_xPAP_in_batch5


title: Huvec_1_TNF


title: Huvec_0_TNF


title: siZCCHC8+ZFC3H1_xPAP_in_batch4


title: Gastroc Pre 21189 [US.1577056]

description:
sample name:
US.1577056

value: Gastrocnemius muscle


title: siZCCHC8+ZFC3H1_noPAP_ip_batch4


title: Huvec_2_Untreated

value: untreated

value: newborn


title: siZCCHC8+ZFC3H1_xPAP_in_batch3


title: Huvec_1_Untreated

value: EUROPE


title: siZCCHC8+ZFC3H1_noPAP_ip_batch3


title: Huvec_0_Untreated

value: Umbilical vein endothelial cells


title: siZCCHC8+ZFC3H1_noPAP_in_batch5


title: siZCCHC8_xPAP_ip_batch1


title: siZCCHC8+ZFC3H1_noPAP_in_batch3


title: Gastroc Post 19832 [US.1576044]

description:
sample name:
US.1576044


title: siZCCHC8+ZFC3H1_noPAP_in_batch4


title: siZCCHC8_xPAP_ip_batch3


title: Map-2_Lane_3

source_name: Escherichia coli

tag: growth medium

value: LB

tag: molecule

value: Plasmid DNA


title: siZCCHC8_xPAP_in_batch3

value: HeLa


title: siZCCHC8_xPAP_in_batch2

value: xPAP


title: siZCCHC8_xPAP_in_batch1


title: siZCCHC8_noPAP_ip_batch3

value: ip


title: Map-2_Lane_2


title: Huvec_4_Untreated

tag: promocell catalogue number

tag: promocell lot number


title: Gastroc Post 23004 [US.1577066]

description:
sample name:
US.1577066

value: Post


title: siZCCHC8_noPAP_ip_batch1


title: Gastroc Post 22130 [US.1577042]

description:
sample name:
US.1577042


title: Map-2_Lane_1