title: BHN5C3BBXX-8

city: Bethesda

first: Chaim

middle: A

last: Schramm

state: MD

address: 40 Convent Dr

department: Vaccine Research Center

institute: NIAID, NIH

description: 81 cells from donor VRC315.06, see README for details

data_processing:
Samples were demultiplexed (see README file) using a custom Java application with a index read PHRED score threshold of 20
Adapters were removed using Trimmomatic-0.32 with parameters `ILLUMINACLIP:nextera.fa:2:30:10:4:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50`
Reads were mapped against a database of human repeat regions using bowtie 2.2.5, and aligned reads were discarded.
Remaining reads were mapped against the hg38 reference using STAR 2.4.2a.
Read counts per gene were quantified using HTSeq 0.6.1 with parameters `-f bam  -m union -r pos -i gene_name -a 10 --stranded no`.
PCA of read counts for all genes were used to identify outlier cells that were excluded from downstream analysis.
MiXCR 2.0 was used with suggested parameters for RNAseq data to reconstruct V(D)J junctions and cells with reported T cell receptor recombinations were removed from downstream analysis.
BraCeR (commit 28e101c) was used to reconstruct full-length BCR sequences and do clonal analysis.
Seurat 2.2.1 was used to analyze gene count data following the recommended practices in the tutorials.
Genome_build: hg38
Supplementary_files_format_and_content: CSV files containing one row per cell and one column per gene. Data is number of reads mapped to each gene in each cell.

source_name: peripheral blood IgG+ memory B cells

extract_protocol:
Smart-seq2 extraction protocol from Picelli et al, Nature Protocols 2014 (doi:10.1038/nprot.2014.006)
RNA was bead-purified from individual cells followed by cDNA synthesis by reverse transcription, template switching and preamplification using KAPA HiFi HotStart ReadyMix.  Indexed libraries were then made by tagmentation and pooled.  Typically, libraries from 75-80 cells were pooled per lane and sequenced with an Illumina HiSeq 3000/4000 paired-end cluster kit on a HiSeq 4000.

value: peripheral blood

value: CD19+ IgG+ memory B cells


title: BHN5C3BBXX-7

status: Public on Jun 20 2019

type: SRA

country: USA

description: 61 cells from donor VRC315.02 and 15 cells from donor VRC315.02, see README for details

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: SS2_15_0160_star_mm10_B21

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

description:
airways
Day 15 BAL T helper cells mouse 1

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Cufflinks to evaluate the expression of transcripts from RefSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file

organism: Mus musculus

source_name: Day 15 BAL T helper cells mouse 1

extract_protocol:
Single memory T helper cells (CD4+CD3+CD44+) sorted directly inflammed tissues (either BAL, lung or mLN) into 2% titron.
SMART-SEQ2 (see Picelli et al 2014)
Single cell RNA-Seq

value: BAL

tag: model

value: HDM


title: S000518.l.rs.lib_re-analyzed

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

institute: Lund University, Sweden

description: re-analysis of GSM2692917

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard.
Alignment was done against hg38 using Novoalign with settings -a TGGAATTCTCGGGTGCCAAGG -l 14 -h -1 -1 -t 90 -g 50 -x 15 -o SAM -o FullNW -r All 51 -e 51
MicroRNA expression was analyzed using custom Perl scripts and calculated as counts per million miRNA reads (cpm).
Genome_build: hg38, mirbase 22 release
Supplementary_files_format_and_content: counts

source_name: Primary breast tumour

extract_protocol:
TRIZOL LS
Small RNA sequencing libraries were prepared from 500 ng total RNA using a protocol analogous with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), but with custom adapters to incorporate dual indexes. Pooled libraries were sequenced on a NextSeq 500 with High Output v2 75 cycle-kits (Illumina)

tag: scan-b external id

tag: sample fullname

value: Primary breast tumour

value: Basal

value: ERneg

value: PRneg

value: High

tag: grade


title: SS2_15_0160_star_mm10_B23


title: S000391.l.rs.lib_re-analyzed

description: re-analysis of GSM2692957

value: LumA

value: ERpos

value: PRpos

value: Low


title: S000397.l.rs.lib_re-analyzed

description: re-analysis of GSM2693019

value: LumB


title: SS2_15_0160_star_mm10_B5


title: SS2_15_0160_star_mm10_B22


title: BHLCVTBBXX-8

description: 94 cells from donor VRC315.06, see README for details


title: BHLCVTBBXX-7

description: 99 cells from donor VRC315.06, see README for details


title: SS2_15_0160_star_mm10_B20


title: S000386.l.rs.lib_re-analyzed

description: re-analysis of GSM2692870


title: SS2_15_0160_star_mm10_B19


title: SS2_15_0160_star_mm10_B18


title: BHLCVTBBXX-5

description: 92 cells from donor VRC315.06, see README for details


title: BHLCVTBBXX-6

description: 95 cells from donor VRC315.06, see README for details


title: SS2_15_0160_star_mm10_B14


title: SS2_15_0160_star_mm10_B15


title: SS2_15_0160_star_mm10_B16


title: SS2_15_0160_star_mm10_B17


title: SS2_15_0160_star_mm10_B13


title: BHLCVTBBXX-4

description: 91 cells from donor VRC315.06, see README for details


title: BHLCVTBBXX-3


title: BHLCVTBBXX-2

description: 93 cells from donor VRC315.06, see README for details


title: S000365.l.rs.lib_re-analyzed

description: re-analysis of GSM2693039


title: SS2_15_0160_star_mm10_B11


title: SS2_15_0160_star_mm10_B1


title: SS2_15_0160_star_mm10_B10


title: S000359.l.rs.lib_re-analyzed2

description: re-analysis of GSM2693010


title: SS2_15_0160_star_mm10_A8


title: SS2_15_0160_star_mm10_A7


title: SS2_15_0160_star_mm10_A9


title: BHLCVTBBXX-1


title: S000359.l.rs.lib_re-analyzed

description: re-analysis of GSM2693009


title: S000357.l.rs.lib_re-analyzed

description: re-analysis of GSM2692970


title: AHHWFKBBXX-6

description: 87 cells from donor VRC315.06, see README for details


title: AHLGN2BBXX-8

description: 104 cells from donor VRC315.05, see README for details


title: SS2_15_0160_star_mm10_A5


title: S000373.l.rs.lib_re-analyzed

description: re-analysis of GSM2693011


title: SS2_15_0160_star_mm10_A6


title: SS2_15_0160_star_mm10_A4


title: S000371.l.rs.lib_re-analyzed

description: re-analysis of GSM2692915


title: S000352.l.rs.lib_re-analyzed

description: re-analysis of GSM2692971


title: S000366.l.rs.lib_re-analyzed

description: re-analysis of GSM2692916


title: S000349.l.rs.lib_re-analyzed

description: re-analysis of GSM2692871


title: SS2_15_0160_star_mm10_A2


title: SS2_15_0160_star_mm10_A3


title: AHLGN2BBXX-6

description: 96 cells from donor VRC315.05, see README for details


title: SS2_15_0160_star_mm10_B12


title: AHLGN2BBXX-7


title: S000342.l.rs.lib_re-analyzed

description: re-analysis of GSM2693037


title: AHLGN2BBXX-5

description: 90 cells from donor VRC315.05, see README for details


title: SS2_15_0160_star_mm10_A24


title: SS2_15_0160_star_mm10_A23


title: SS2_15_0160_star_mm10_A22


title: SS2_15_0160_star_mm10_A21


title: SS2_15_0160_star_mm10_A20


title: S000330.l.rs.lib_re-analyzed

description: re-analysis of GSM2692914


title: SS2_15_0160_star_mm10_A1


title: 192MGS3

city: Cambridge

first: Mark

last: Charlton-Perkins

address: Tennis court rd

country: United Kingdom

institute: University of Cambridge

data_processing:
Trimmomatic (read trimming)
Hisat2 genome aligment
Samtools Sam to Bam sorting
Bioconuducter (Feature counts, Rsubread, limma,DESeq2, DEFormats, org.Dr.eg.db, EdgeR)
Genome_build: GRCz10
Supplementary_files_format_and_content: TMM fold change analysis

organism: Danio rerio

source_name: 192hpf_GFAP:GFP Positive

extract_protocol:
Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia (GFP) and control retinal tissue (non-GFP). Cells were sorted into lysis buffer, and RNA was immediately extracted using the RNeasy mini kit (Qiagen).
RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 (NuGEN) using manufacturer’s protocol.
Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions

tag: age

tag: genotype

value: Control (GFAP:GFP)

value: Dissociated retinal tissue

tag: gfap

value: Positive


title: AHLGN2BBXX-3

value: peripheral blood


title: S000324.l.rs.lib_re-analyzed

description: re-analysis of GSM2692880


title: AHLGN2BBXX-4

description: 75 cells from donor VRC315.05, see README for details

value: CD19+ IgG+ memory B cells


title: 192MGS2


title: S000316.l.rs.lib_re-analyzed

description: re-analysis of GSM2693018


title: SS2_15_0160_star_mm10_A19

value: BAL


title: S000323.l.rs.lib_re-analyzed

description: re-analysis of GSM2692878


title: 192CS3

source_name: 192hpf_GFAP:GFP Negative

value: Negative


title: 192MGS1


title: AHLGN2BBXX-2

description: 89 cells from donor VRC315.05, see README for details


title: SS2_15_0160_star_mm10_A18

value: HDM


title: S000310.l.rs.lib_re-analyzed

description: re-analysis of GSM2692913

value: Primary breast tumour


title: AHKYC5BBXX-8

description: 88 cells from donor VRC315.05, see README for details


title: 192CS2


title: SS2_15_0160_star_mm10_A15


title: AHKYC5BBXX-6

description: 92 cells from donor VRC315.05, see README for details


title: S000309.l.rs.lib_re-analyzed

description: re-analysis of GSM2692912


title: S000306.l.rs.lib_re-analyzed

description: re-analysis of GSM2692877


title: 120MGS3

source_name: 120hpf_GFAP:GFP Positive


title: 192CS1


title: S000304.l.rs.lib_re-analyzed

description: re-analysis of GSM2692969


title: AHLGN2BBXX-1

description: 86 cells from donor VRC315.05, see README for details


title: SS2_15_0160_star_mm10_A16


title: S000297.l.rs.lib_re-analyzed

description: re-analysis of GSM2693036


title: SS2_15_0160_star_mm10_A14


title: S000295.l.rs.lib_re-analyzed

description: re-analysis of GSM2692879

value: ERneg


title: 120MGS2


title: BHHVK2BBXX-8

description: 81 cells from donor VRC315.02, see README for details


title: 120MGS1


title: AHKYC5BBXX-5

description: 72 cells from donor VRC315.05, see README for details


title: BHHVK2BBXX-7

description: 77 cells from donor VRC315.02, see README for details


title: S000276.l.rs.lib_re-analyzed

description: re-analysis of GSM2692873

value: PRneg


title: AHKYC5BBXX-7

description: 82 cells from donor VRC315.05, see README for details


title: 120CS3

source_name: 120hpf_GFAP:GFP Negative


title: SS2_15_0160_star_mm10_A11

description:
airways
Day 15 BAL T helper cells mouse 1


title: S000275.l.rs.lib_re-analyzed

description: re-analysis of GSM2693008


title: SS2_15_0160_star_mm10_A10


title: BHHVK2BBXX-5

description: 79 cells from donor VRC315.02, see README for details


title: BHHVK2BBXX-6

description: 84 cells from donor VRC315.02, see README for details


title: S000272.l.rs.lib_re-analyzed

description: re-analysis of GSM2692872


title: 120CS1


title: S000271.l.rs.lib_re-analyzed

description: re-analysis of GSM2692881


title: 96MGS3

source_name: 96hpf_GFAP:GFP Positive


title: BHHVK2BBXX-4

description: 73 cells from donor VRC315.02, see README for details


title: FP_Input_ChIP-Seq

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

country: China

institute: Tianjin Medical University

library_source: genomic

data_processing:
ChIP-Seq data were mapped to mouse reference genome (mm10) by bowtie2
ChIP-Seq peaks were generated using peak finding algorithm MACS2 (Model-based Analysis for ChIP -Seq, version: macs2 2.1.1.20160309)
Genome_build: mm10
Supplementary_files_format_and_content: bdg files were generated by MACS2

molecule: genomic DNA

source_name: Mouse kidney

extract_protocol:
Frozen kidneys were briefly homogenized. Then tissues were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with Pol II antibody (CST, 14958). After elution and reversal cross-linking, DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

value: kidney

tag: strain

tag: chip antibody


title: SS2_15_0160_star_mm10_A13


title: S000267.l.rs.lib_re-analyzed

description: re-analysis of GSM2692911

value: LumA


title: BHHVK2BBXX-2


title: 96MGS2


title: BHHVK2BBXX-3


title: 96MGS1


title: S000264.l.rs.lib_re-analyzed

description: re-analysis of GSM2693035

value: ERpos

value: High


title: SS2_15_0160_star_mm10_A12


title: S000251.l.rs.lib_re-analyzed

description: re-analysis of GSM2692968


title: 96CS3

source_name: 96hpf_GFAP:GFP Negative


title: 120CS2


title: BHFL3MBBXX-8

description: 67 cells from donor VRC315.02, see README for details


title: S000156.l.rs.lib_re-analyzed

description: re-analysis of GSM2692910

value: Basal


title: FP_PolII_ChIP-Seq


title: PKD_PolII_ChIP-Seq


title: BHFL3MBBXX-7


title: WT_PolII_ChIP-Seq


title: 96CS2


title: PKD_Input_ChIP-Seq


title: S000141.l.rs.lib_re-analyzed

description: re-analysis of GSM2692909

value: PRpos


title: WT_Input_ChIP-Seq


title: 72MGS3

source_name: 72hpf_GFAP:GFP Positive

value: Control (GFAP:GFP)


title: 96CS1

value: Dissociated retinal tissue


title: AH5W2NBBXX-6

description: 51 cells from donor VRC315.02, see README for details


title: SS2_15_0160_star_mm10_A17


title: HFSC-Ring1b_ChIPseq

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

data_processing:
bcl2fastq v2 for basecalling
Adaptors and the last nucleotide (the number 51) were removed and reads where mapped to mm9 using 1. tophat (v2.1.1) with parameters  --no-coverage-search --library-type fr-unstranded  (RNA-seq) and using bowtie v1.2.2  with default parameters without allowing for multi-mapping (-m 1).
PCR duplicates were removed using picard tools (1.62) and read counts per gene were calculated using Htseq-count (v0.7.2) with parameters -q -t exon --stranded=no --mode=intersection-nonempty using the Refseq gtf from UCSC. For ChIP-seq, peaks were called using MACS2 v2.1.1 with parameters -g mm --nomodel -p 1e-10 –B
Genes with 0 counts in all samples were removed and differential analysis was performed using DESeq2 (v3.7) with default parameters. Genes with an absolute log2FC >= 1 and FDR <= 0.1 were considered as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized_countTable.txt contains the normalized counts produced by DESeq2
Supplementary_files_format_and_content: WTvsRing1KO_HFSC_logfc1.txt contains the output of DESeq2 plus a column indicating if a gene is differentially expressed using the threshold determined for the study ( abs (log2fc) >= 1 and fdr =< 0.1 )
Supplementary_files_format_and_content: HFSC-Ring1b_peaks.narrowPeak ontains called peaks by MACS2 in HFSC
Supplementary_files_format_and_content: ISC-Ring1b_peaks.narrowPeak contains called peaks by MACS2 in ISC
Supplementary_files_format_and_content: Differential expression analysis results: WTvsRing1KO_HFSC_logfc1.txt
Supplementary_files_format_and_content: Raw counts: HFSC_Ring1bKO_counts.txt
Supplementary_files_format_and_content: Normalized counts by deseq2: Normalized_countTable.txt

source_name: Hair Follicle Stem Cells

extract_protocol: nagen synchronized hair follicles from LGR5-Ring1a/b ++ mice were extracted following the protocol previously described. Single cells were resuspended in Sorting medium (as previously described) and LGR5-GFP positive cells were FACS-sorted with either FACS-Melody (BD FACSMelody Cell Sorter) or FACS-Jazz (BD FACSJAZZ Cell Sorter), discriminating only singlets (plotting Area vs Height on both SSC and FSC) and only alive cells with Propidium Iodide. An amount of 2.5 Milion cells were resuspended and sonicated with Branson Digital Sonifier (Branson) in IP buffer (SDS Buffer: Triton Buffer 2:1 – SDS Buffer (NaCl 100mM, Tris-HCl pH 8.1 50mM, NaN3 0.2%, SDS 0.5%); Triton Buffer ( NaCl 100mM, Tris-HCl pH 8.6 100mM, EDTA 5mM, NaN3 0.2%, Triton X-100 5%). Sonicated chromatin were incubated with 10ug of Ring1b antibody generated in the lab (Chiacchiera, Rossi, Sriganesh Jammula, et al. 2016) over night and the immunocomplexes were recovered by magnetic beads (Dynabeds, Life-technologies) and decrosslinked over night with NaHCO3 0.1M and 1% SDS. Decrosslinked DNA were purified.

tag: tisse

value: hair follicle

value: home-made lab (Chiacchiera, Rossi, Sriganesh Jammula, et al. 2016)

value: WT


title: ISC-Ring1b_ChIPseq

source_name: Intestinal Stem Cells

extract_protocol: Intestinal epithelium from LGR5-Ring1a/b ++ mice was extracted following the protocol previously described. Single cells were resuspended in Sorting medium (as previously described) and LGR5-GFP positive cells were FACS-sorted with either FACS-Melody (BD FACSMelody Cell Sorter) or FACS-Jazz (BD FACSJAZZ Cell Sorter), discriminating only singlets (plotting Area vs Height on both SSC and FSC) and only alive cells with Propidium Iodide. An amount of 2.5 Milion cells were resuspended and sonicated with Branson Digital Sonifier (Branson) in IP buffer (SDS Buffer: Triton Buffer 2:1 – SDS Buffer (NaCl 100mM, Tris-HCl pH 8.1 50mM, NaN3 0.2%, SDS 0.5%); Triton Buffer ( NaCl 100mM, Tris-HCl pH 8.6 100mM, EDTA 5mM, NaN3 0.2%, Triton X-100 5%). Sonicated chromatin were incubated with 10ug of Ring1b antibody generated in the lab (Chiacchiera, Rossi, Sriganesh Jammula, et al. 2016) over night and the immunocomplexes were recovered by magnetic beads (Dynabeds, Life-technologies) and decrosslinked over night with NaHCO3 0.1M and 1% SDS. Decrosslinked DNA were purified.

value: Intestine


title: S000131.l.rs.lib_re-analyzed

description: re-analysis of GSM2692967

value: LumB

value: Low


title: RNA-seq_D3-MoDC-R

city: New York

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

description: RNA seq CD14+ Monocytes cultured in GM-CSF

data_processing:
Sequenced reads were mapped to reference human genome (hg38 assembly) using STAR aligner (2.5.3, Dobin et al., 2013 Bioinformatics) with the following parameters: STAR --runThreadN 8 --genomeDir STARIndex --readFilesIn ${j}_R1_001.fastq.gz --readFilesCommand zcat --outFileNamePrefix rnaseq_STAR/${j}.STAR --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --sjdbGTFfile GRCh38_gencode_release29/annotation/genes.gtf --quantMode GeneCounts. The count file matrix was fed into SARTools 1.3.0 DESeq2 or HSS RNA-seq visualization platform (1.3.1) package to obtain differentially gene expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: Tab limited raw HT-seq counts

molecule: polyA RNA

source_name: CD14+ Monocytes

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep kit(E7765L)

treatment_protocol: CD14+ cells cultured in M-CSF (20ng/ml) were treated with or without LPS (0.1 ng/ml) overnight and then stimulated with IFN-γ (100 U/ml) for 3 hours and cells cultured in GM-CSF (20 ng/ml) were treated with or without IFN-γ (100 U/ml) for 48 hours and then stimulated with LPS (10 ng/ml) for 3 hours

value: CD14+ Monocytes

tag: cultured in

value: GM-CSF

tag: treatment

value: NT

tag: donor


title: S000127.l.rs.lib_re-analyzed

description: re-analysis of GSM2692966

value: Primary breast tumour


title: RNA-seq_D3-MoDC-G


title: HFSC-WT-rep1_RNAseq

extract_protocol: FACS-sorted Cells were collected in 0.5mL Eppendorf and processed directly following SMART-seq2 protocol as described in Picelli et al., 2011 with minor modifications. Briefly, 3000 cells per sample were collected and fudge to pellet them, supernatant were removed and cells were directly lysed in  2ul of lysis buffer (0.2% Triton X-100, 4U/uL RNase inhibitor). 1uL of 10uM oligo-dT30Vn and 1uL of 10mM dNTPs were added pipetting well and the samples were incubated 3min ad 72°C. RT step were performed as described in the paper with Superscript III reverse transcriptase enzyme (Invitrogen). Pre-amplification of the obtained cDNA were performed with KAPA HotStart Taq enzyme with High Fidelity buffer. Pre-amplified cDNA were purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter) using Invitrogen Magnet, concentration were assayed with Qubit (Thermo-Fisher Q33216) dsDNA High sensitivity reagents  (Qubit™ dsDNA HS Assay Kit, Thermo-Fisher Q32851)  and quality were verified by Bioanalyzer (Agilent) using Dna High sensitivity kit. 2 nanograms of cDNA were tagmented with100ng of home made Tn5 enzyme and further amplified with KAPA (Kapa HiFi Hotstart KIT). Tagmented amplified DNA were purified with Ampure beads (Agencourt AMPure XP- Beckman Coulter) and the quality of obtained library were controlled at Bioanalyzer with DNA HS assay, loading 1ug of sample, prior sequencing.


title: S000109.l.rs.lib_re-analyzed

description: re-analysis of GSM2693007

value: LumA


title: 72MGS2

value: Positive


title: BHHVK2BBXX-1

description: 83 cells from donor VRC315.02, see README for details

value: peripheral blood

value: CD19+ IgG+ memory B cells


title: S000062.l.rs.lib_re-analyzed

description: re-analysis of GSM2693006

value: Basal

value: ERneg

value: PRneg

value: High


title: RNA-seq_D3-MoDC-GL


title: HFSC-RingKO-rep2_RNAseq

value: hair follicle


title: HFSC-WT-rep2_RNAseq

value: WT


title: 72MGS1

value: Control (GFAP:GFP)

value: Dissociated retinal tissue


title: RNA-seq_D2-MoDC-R


title: 72CS1

source_name: 72hpf_GFAP:GFP Negative

value: Negative


title: S000046.l.rs.lib_re-analyzed

description: re-analysis of GSM2693005

value: ERpos

value: PRpos

value: Low


title: S000057.l.rs.lib_re-analyzed

description: re-analysis of GSM2692956

value: Primary breast tumour

value: LumB


title: 72CS2


title: 72CS3


title: RNA-seq_D2-MoDC-L

value: CD14+ Monocytes

value: GM-CSF


title: RNA-seq_D2-MoDC-G


title: 60MGS3

source_name: 60hpf_GFAP:GFP Positive

value: Positive


title: S000039.l.rs.lib_re-analyzed

description: re-analysis of GSM2693034

value: Basal


title: S000045.l.rs.lib_re-analyzed

description: re-analysis of GSM2693004


title: RNA-seq_D3-MoDC-L


title: KO_8c_F7 [libB.F7]

city: Stockholm

first: Pauliina

last: Damdimopoulou

address: Karolinska University Hospital OBGY K57

institute: Karolinska Institute

data_processing:
The libraries were sequenced by two lanes of Illumina HiSeq2000 instrument. The sequenced raw STRT reads were processed by STRTprep [PMID: 26874359]; v3dev branch, d7efcde commit (https://github.com/shka/STRTprep/tree/v3dev) to demultiplex according to the barcode, and to exclude redundant reads according to the UMI; sequence of the template switching oligo (UMI, barcode and tri-G) were trimmed.
The resulting bam files were converted to tag directories using Homer.
A gft file comprising annotations retrieved from UCSC and the ERCC annotations, was used to estimate the reads in all annotated genes using Homer.
Genome_build: Mm9
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts of annotated genes and ERCC controls

source_name: Embryos

growth_protocol: Sexually mature knockout and wildtype females were superovulated by i.p. injections of 5 IU pregnant mare serum (Folligon; Intervet, Dublin, Ireland), followed two days later by 5 IU human chorionic gonadotropin (hCG) (Chorulon; Intervet, Dublin, Ireland), and mated with trained WT studs. Oocytes (no mating) and zygotes were collected from oviducts the following morning. Cumulus cells were removed with hyaluronidase (0.3 mg/ml, Sigma-Aldrich, St.Louis, MO, USA) treatment. placed in KSOM medium (EMD Millipore, Nottingham, UK) under ovoil-100 (Vitrolife) in IVF 4-well plates (Sigma-Aldrich) for culture at 37°C under 5% CO2/95% air. Embryos were picked 21-23 h post hCG treatment (MII oocytes, no culture), 45-47 hpf (2-cell stage) and 7173 hpf (8-cell stage) on three different occasions, yielding a total of 16 zygotes, 14 2-cell stage embryos, and 15 8-cell stage embryos for both maternal Plag1 knockout and wildtype.

extract_protocol:
No extraction.
Single embryos or uncultured oocytes were picked into 4 ml library lysis buffer containing 5 mM Tris-HCl pH 8.0 (Sigma-Aldrich), 2 mM dNTP mixture (ThermoFisher Scientific, Waltham, MA, USA), 10 mM DTT (Sigma-Aldrich), 0.05% Triton X-100 (Sigma-Aldrich), 400 nM anchored oligo(dT) primer biotin-TTAAGCAGTGGTATCAACGCAGAGTCGAC(T)29V where V is LNA nucleotide (Exiqon, Vedbaek, Denmark), and 4 U RiboLock RNase inhibitor (ThermoFisher). Two separate 46-plex libraries (libA and libB) were made as described previously (Krjutskov et al. 2016 Hum Reprod 31:844) with the following modifications: barcoded 10 µM template-switching oligonucleotides were added prior to reverse transcriptase, ERCC spike-in Mix A was diluted 15,300-fold with clean water, and 1 µl was taken per library reverse transcriptase master mix. Twenty cycles of PCR were used for the first round of amplification and ten additional cycles for the second round to introduce Illumina-compatible universal sequences. Both libraries contained all developmental stages and genotypes.

treatment_protocol: No treatment.

value: Plag1 knockout

tag: developmental stage


title: KO_8c_F8 [libB.F8]


title: 60MGS2


title: 60MGS1


title: RNA-seq_D2-MoDC-GL


title: RNA-seq_D1-MoDC-R

value: NT


title: KO_8c_F5 [libB.F5]


title: S000036.l.rs.lib_re-analyzed

description: re-analysis of GSM2693033

value: LumA


title: S000034.l.rs.lib_re-analyzed

description: re-analysis of GSM2693032

value: High


title: RNA-seq_D1-MoDC-L


title: WT_8c_F4 [libB.F4]

value: WT


title: HFSC-RingKO-rep1_RNAseq

value: hair follicle


title: 60CS2

source_name: 60hpf_GFAP:GFP Negative

value: Control (GFAP:GFP)

value: Dissociated retinal tissue


title: S000019.l.rs.lib_re-analyzed

description: re-analysis of GSM2693017

value: ERpos


title: RNA-seq_D1-MoDC-G


title: RNA-seq_D1-MoDC-GL


title: S000017.l.rs.lib_re-analyzed

description: re-analysis of GSM2692965

value: PRpos


title: 60CS1

value: Negative


title: WT_8c_F2 [libB.F2]


title: S000009.l.rs.lib_re-analyzed

description: re-analysis of GSM2693031

value: Primary breast tumour

value: Low


title: WT_8c_F3 [libB.F3]


title: KO_8c_F6 [libB.F6]


title: RNA-seq_LPS-IFNG-3

description: RNA seq CD14+ Monocytes

value: CD14+ Monocytes

value: M-CSF


title: 48MGS2

source_name: 48hpf_GFAP:GFP Positive

value: Positive


title: 48MGS3


title: KO_8c_E7 [libB.E7]


title: 48MGS1


title: 60CS3


title: MDAMB231 parental cell line (control), Replicate 2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1).  Quality trimming was not performed.
The concatenated sequences were directly aligned to the Homo sapiens hg38 reference genome assembly (hg38.fa) using tophat2 (version 2.0.13)
Differentially expressed genes were identified for the two pairwise comparisons: MCF7_Palbociclib vs. MCF7_Parental and  MDA_Palbociclib vs. MDA_Parental,  using the tuxedo suite of programs including cufflinks-cuffdiff2 (version 2.2.1).
A  q-value cutoff ≤ 0.05 with |log2FC|  was used to determine differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: fpkm normalized expression

source_name: MDAMB231 parental cell line (control)

growth_protocol: MCF7 (HTB-22) and MDA-MB-231 (HTB-26) cells were purchased from the American Type Culture Collection (ATCC) and maintained at 37ºC with 5% CO2. MCF7 and MDA-MB-231 cells were cultured in IMEM (Corning) supplemented with 10% fetal bovine serum (FBS, Invitrogen).

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s instructions.
Libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) or Set B (Cat# RS-122-2102) with poly-A enrichment.

treatment_protocol: Drug resistant cells were established by culturing in media containing palbociclib (0.1-4uM). Drug was replenished every 3 days. Cells were subcultured every 1-2 weeks with 25% increments in drug concentration. The resistant cells were established after 6 months and maintained in the presence of 1uM palbociclib.

tag: cell line

value: ER- breast cancer cell line

tag: resistance


title: MDAMB231 parental cell line (control), Replicate 3

tag: cell type


title: 48CS3

source_name: 48hpf_GFAP:GFP Negative

tag: tissue


title: MDAMB231 parental cell line (control), Replicate 1


title: RNA-seq_LPS-IFNG-2

description: RNA seq CD14+ Monocytes


title: RNA-seq_IFNG-3h-3

description: RNA seq CD14+ Monocytes


title: 48CS2


title: MDAMB231 palbociclib resistant, Replicate 3

source_name: MDAMB231 palbociclib resistant

value: palbociclib


title: KO_8c_E6 [libB.E6]

value: Plag1 knockout


title: MDAMB231 palbociclib resistant, Replicate 2


title: RNA-seq_IFNG-3h-2

description: RNA seq CD14+ Monocytes


title: WT_8c_E4 [libB.E4]


title: 48CS1


title: RNA-seq_IFNG-3h-1

description: RNA seq CD14+ Monocytes


title: MDAMB231 palbociclib resistant, Replicate 1


title: RNA-seq_LPS-16h-3

description: RNA seq CD14+ Monocytes


title: WT_8c_E3 [libB.E3]


title: WT_8c_F1 [libB.F1]


title: RNA-seq_LPS-IFNG-1

description: RNA seq CD14+ Monocytes


title: MCF7 parental cell line (control), Replicate 2

source_name: MCF7 parental cell line (control)

value: ER+  breast cancer cell line


title: RNA-seq_LPS-16h-2

description: RNA seq CD14+ Monocytes


title: WT_8c_E1 [libB.E1]


title: KO_2c_D8 [libB.D8]


title: RNA-seq_LPS-16h-1

description: RNA seq CD14+ Monocytes


title: KO_8c_E5 [libB.E5]


title: MCF7 parental cell line (control), Replicate 1


title: RNA-seq_Resting3

description: RNA seq CD14+ Monocytes

value: NT


title: KO_2c_D7 [libB.D7]


title: MCF7 palbociclib resistant, Replicate 3

source_name: MCF7 palbociclib resistant


title: RNA-seq_Resting2

description: RNA seq CD14+ Monocytes


title: RNA-seq_Resting1

description: RNA seq CD14+ Monocytes


title: KO_2c_D6 [libB.D6]


title: KO_2c_D5 [libB.D5]


title: MCF7 palbociclib resistant, Replicate 2


title: MCF7 parental cell line (control), Replicate 3


title: WT_8c_E2 [libB.E2]

value: WT


title: KO_2c_D4 [libB.D4]


title: OMM (Outer Mito. Membrane) + Nocodazole 30min Control 2

city: Stanford

first: Furqan

middle: M

last: Fazal

state: California

address: 269 Campus Drive, CCSR 2130

department: Genetics

institute: Stanford University

description:
See protocols section
OMM-noco-30min-C2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt

data_processing:
The RNA-seq reads were initially subject to barcode removal and primer trimming using a published script (Flynn et al., Nature Protocols 2016) based on Trimmomatic: (https://github.com/qczhang/icSHAPE/blob/master/scripts/trimming.pl): perl trimming.pl -1 $fastq-file1 -2 $fastq-file2 -p $trimmed-file1 -q $trimmed-file2 -l 0 -t 0 -c phred33 -a adapter.fa -m 36
The reads were then mapped using STAR (Dobin et al., Bioinformatics 2013) to the GRCh38 Ensembl genome, with Homo_sapiens.GRCh38.84.gtf annotations (http://uswest.ensembl.org/index.html), using the following command: STAR --genomeDir ~/genome/human/star --runThreadN 8 --readFilesIn $trimmed-file1 $trimmed-file2 --outFileNamePrefix $output-samfile
The mapped reads were then counted using HTSEQ (Anders et al., Bioinformatics 2015) : python -m HTSeq.scripts.count -m intersection-nonempty -s reverse -i gene_id $output-samfile ~/genome/human/Homo_sapiens.GRCh38.84.gtf > $txt
The mapped data was visualized using the UCSC browser track. To generate genome tracks we used samtools to generate stranded BAM files for each library from the SAM file. The BAM file was then used to generate a bedgraph following the command: genomeCoverageBed -bg -split -ibam $bam -g ~/genome/human/star/chrNameLength.txt > $bed_file
Genome_build: hg38
Supplementary_files_format_and_content: Tab-deliminted text files include either DESEQ2 log2foldchanges and Padjusted values; or count data from STAR and HTSEQ. Differentially-expressed genes were determined using DESeq2 (Love et al., Genome Biology 2014), using FDR < 0.05 and 18 controls. All P-values from DESeq2 are FDR adjusted for multiple-hypothesis testing. For the OMM perturbation experiments, we used the same 18-control strategy, but replacing the unperturbed OMM APEX-seq and NES APEX-seq values with the corresponding drug-perturbed values. There were two exceptions to the 18-control approach in all our analysis. For the LMA gene in nuclear lamina, and the SENP2 gene in the nuclear pore construct, the unlabeled control had high counts for these genes in the RNA-seq data, as these genes were used to target APEX to the corresponding location. Therefore, to compensate, we replaced the LMA 18-control DESeq2 log2fold change with the 2-control log2fold change (using LMA controls) in the LMA data; we did the same for SENP2 in the nuclear pore dataset. Otherwise, all other data was as is.

growth_protocol: HEK 293T cells from the ATCC (passages < 25) were cultured in a 1:1 DMEM/MEM mixture (Cellgro) supplemented with 10% fetal bovine serum, 100 units/mL penicillin, and 100 mg/mL streptomycin at 37oC under 5% CO2.

extract_protocol:
To labeled and unlabeled (controls) HEK 293T cells in 10-cm plates, we added ~1 ml DPBS containing 5 mM Trolox and 10 mM sodium ascorbate, as well as ~4 ul Ribolock RNAse inhibitor (Thermo Fischer). The cells were then scrapped off 10-cm plates using cell lifters (Corning), transferred to 2-ml Eppendorf tubes, and spun at 500G for 4 minutes to pellet cells. The supernatant was removed, and the cells were processed using the RNeasy plus mini kit (Qiagen) following the manufacture protocol, including adding beta-mercaptoethanol to the lysis buffer. The cells were sent through the genomic DNA (gDNA) eliminator column supplied with the kit. One modification to the protocol was replacing the RW1 buffer with RWT buffer (Qiagen) for washing. The extracted RNA was eluted into RNAse-free water, and RNA integrity was checked using the Agilent bioanalyzer 2100 using the “high-sensitivity” setting. Only RNA with a RIN (RNA integrity number) > 8.5 was used for subsequent experiments. RNAs shorter than 100 nt were not efficiently recovered.
RNA-seq libraries were prepared from enriched RNA (corresponding to ~30-50 µg of pre-enriched RNA) using the Illumina TruSeq Stranded mRNA Protocol, which included polyA+ selection. The prepared libraries were stranded and were quality-controlled by sequencing on the Illumina MiSeq. Good libraries (> 80% unique reads) were sequenced on the Illumina Hiseq400 at ~35 million paired (2 x 75) reads per library. The correlation between biological replicates was high (between 0.96 and 1). For the MITO APEX-seq we also generated total RNA samples (by omitting the polyA+ selection step in the TruSeq protocol), as well as a polyA+ selected technical replicate for 1 of the labeled samples.

treatment_protocol: 18-24 hrs after plating HEK 293T cells stably expressing the corresponding APEX2 fusion construct, APEX labeling was initiated by changing the medium to fresh medium containing 500 uM biotin-phenol (Iris Biotech GMBH). This was incubated at 37oC under 5% CO2 for 30 minutes. H2O2 (Sigma Aldrich) was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 minute (Rhee et al., Science 2013). The reaction was quenched by replacing the medium with an equal volume of 5 mM Trolox, 10 mM sodium ascorbate and 10 mM sodium azide in Dulbecco's phosphate-buffered saline (DPBS). Cells were washed with DPBS containing 5 mM Trolox and 10 mM sodium ascorbate three times before proceeding to imaging, RT-qPCR or RNA-seq experiments. The unlabeled controls were processed identically, except that the H2O2 addition step was omitted.

tag: protocol

value: APEX-seq

tag: cell compartment

value: Outer Mitochondrial Membrane


title: 201B7_2

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.16
The sequenced reads were mapped to the hg38 human reference genome using Tophat2 (version 2.1.1) with the human GENCODE (version 27) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
RPKM values were determined by Cufflinks version 2.2.1 package with the human GENCODE (version v27, protein coding) annotation gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include RPKM values for each sample.

source_name: hiPSC

extract_protocol:
RNAeasy plus Mini Kit (QIAGEN) for RNA.
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: hiPSC

tag: analysis method

value: RNA-seq


title: MCF7 palbociclib resistant, Replicate 1


title: 201B7_1


title: KO_2c_D3 [libB.D3]


title: KO_2c_D2 [libB.D2]


title: HDF1388_2

source_name: HDF

value: HDF


title: siRNA #8 for HOXA5 short RNA

type: RNA

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

institute: Tokushima University Graduate school

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA was extracted using RNAiso Plus reagent (Takara).

treatment_protocol: HCT116 cells were treated with two siRNAs (#7 and #8) targeting HOXA5 short RNA for 48 h, respectively.

value: HCT116 colon cancer cell line

value: HOXA5 short RNA silencing


title: siRNA #7 for HOXA5 short RNA


title: 21F1 iPS

city: Kobe City

first: Michiyo

last: Koyanagi-Aoi

address: Chuo-ku, Kusunoki-cho 7-5-1

institute: Kobe University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip primeview human gene expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000 7G system.

data_processing: The data were analyzed using the Gene Spring GX 13.1.1 software program (Agilent Technologies). We used RMA as summarization algorithm and performed quantile normalizaion. Baseline transformation was not performed.

label: biotin

source_name: iPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of total RNA

growth_protocol: iPSCs were cultured in StemFit medium on plates coated with laminin-511 E8 fragments.

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

tag: gender

value: female

value: iPS

tag: origin

value: Fibro (TIG120)

tag: method

value: Sendai virus


title: 201B7 iPS

source_name: validated iPS

value: Fibro (HDF1388)

value: retrovirus


title: OMM (Outer Mito. Membrane) + Nocodazole 3min Control 2

description:
See protocols section
OMM-noco-3min-C2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: control_differentiation #4

city: Leuven

first: Pierre

last: Vanderhaeghen

address: O&N4 Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

data_processing:
paired-end reads per sample were mapped against the mouse reference genome using STAR 2.5.3a
gene level counts were obtained using HTSeq 0.9.1
level of differential gene expression was calculated using EdgeR 3.20.1
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and normalized abundance measurements

source_name: cortical progenitor cells

growth_protocol: The A2 lox.Cre Bcl6 cell lines, tetracyclin-inducible Bcl6 ICE (A2lox.Cre) mouse Embryonic Stem Cells were routinely propagated on irradiated mouse embryonic fibroblasts in DMEM supplemented with 15% ESC-certified fetal bovine serum (vol/vol), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol, 50 U.ml−1 penicillin/ streptomycin and 10E3 U.ml−1 mouse Leukemia Inhibitor Factor. For differentiation, A2 lox.Cre Bcl6 mouse ESCs were plated at low density (20 × 10E3 ml−1) on gelatin-coated 5-cm dishes (day -1). At day 0, the ES medium was changed to DDM medium. At day 2, DDM was supplemented with cyclopamine (400 ng/mL) and the medium was replenished every 2 days. After 10 days, medium was switched back to DDM (Gaspard et al., 2009).

extract_protocol:
Total mRNA was extracted using the QIAGEN RNeasy mini kit
the indexed cDNA libraries were prepared using the TruSeq stranded mRNA Library Preparation kit (Illumina)

treatment_protocol: differentiation day 12, 24h Bcl6 induction using 1 µg.ml−1 Doxycline treatment or DMSO (control)

tag: cell types

value: ES-cell derived A2 lox.Cre Bcl6 progenitor cells

value: DMSO

tag: differentiation day

value: day 12


title: Bcl6_differentiation #3

value: Doxycycline


title: control siRNA

tag: genotype

value: control


title: Bcl6_differentiation #4


title: OMM (Outer Mito. Membrane) + Nocodazole 30min Control 1

description:
See protocols section
OMM-noco-30min-C1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt

value: APEX-seq

value: Outer Mitochondrial Membrane


title: KO_2c_D1 [libB.D1]

value: Plag1 knockout


title: OMM (Outer Mito. Membrane) + Nocodazole 3min Control 1

description:
See protocols section
OMM-noco-3min-C1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: HOXA5 short RNA transfected cells

treatment_protocol: HCT116 cells were transfected with a pEB vector containing HOXA5 short RNA, and then, the cells were cultured in selection medium (Blastcidin) for 2 weeks.

value: overexpression of HOXA5 short RNA


title: mock transfected cells

value: HCT116 colon cancer cell line


title: control_differentiation #3


title: OMM (Outer Mito. Membrane) + Nocodazole 2hr Target 2

description:
See protocols section
OMM-noco-2hr-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: HDF1388_1

value: HDF

value: RNA-seq


title: OSKM-NPC_tumor_210

source_name: OSKM-NPC (PSA-NCAM positive)-derived tumor

value: 201B7-derived cells


title: Bcl6_differentiation #2


title: OSKM-NPC_tumor_179


title: WT_2c_C8 [libB.C8]

value: WT


title: WT_2c_C7 [libB.C7]


title: control_differentiation #2


title: OMM (Outer Mito. Membrane) + Nocodazole 2hr Target 1

description:
See protocols section
OMM-noco-2hr-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: OMM (Outer Mito. Membrane) + Nocodazole 30min Target 2

description:
See protocols section
OMM-noco-30min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: WT_2c_C6 [libB.C6]


title: Bcl6_differentiation #1


title: OSKM-NPC_tumor_173


title: MYC-NPC_tumor_174

source_name: MYC-NPC (PSA-NCAM positive)-derived tumor


title: WT_2c_C5 [libB.C5]


title: WT_2c_C4 [libB.C4]


title: OMM (Outer Mito. Membrane) + Nocodazole 30min Target 1

description:
See protocols section
OMM-noco-30min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: OMM (Outer Mito. Membrane) + Nocodazole 9min Target 2

description:
See protocols section
OMM-noco-9min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: MYC-NPC_tumor_137


title: MYC-NPC_tumor_148


title: WT_2c_C3 [libB.C3]


title: rip_input_panx

first: Martin

middle: Heinrich

last: Fabry

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: Cancer Research UK, Cambridge Institute

description:
Sample 44
Flies expressing GFP-Panx.

data_processing:
Library strategy: RIP-seq
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, for RIP-seq the first 5 bases of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). After removal of rRNA mapped reads, high-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6; downloaded from Flybase) using STAR (Dobin et al. 2013). For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outMultimapperOrder Random' and non-mapping reads were removed. Alignment files were then converted back to fastq format with samtools (Li et al. 2009) and re-aligned to the transposon consensus sequences allowing multi-mappers that were assigned to a random position. Generated bam alignment files were indexed using samtools index. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads.
Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage function with 10 bp bin sizes (Ramirez et al. 2016). Reads mapping to genes were counted with htseq (Anders et al. 2015) and transposon derived reads were calculated using a custom script. Differential expression analysis was performed using custom built R scripts.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files for all dm6 alignment files, normalized to rpm. For RNA- and smallRNA-seq, sequences were split in sense- and antisense-mapping reads before normalization.

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: Flies were grown at 25°C.

extract_protocol:
Samples were crosslinked in formaldehyde and lysed, followed by sonication and immunoprecipitation with GFP-trap magnetic beads (Chromotek).
SMARTer stranded RNA-seq Kit (Clontech).

tag: strain/cell line background

tag: tissue/cell type

value: ovary

tag: genotype/variation

value: GFP-Panx

tag: rip antibody


title: rip_panx

description:
Sample 45
Flies expressing GFP-Panx.

value: GFP-trap magnetic beads


title: WT_2c_C2 [libB.C2]

source_name: Embryos

tag: developmental stage


title: NCAM-NPC_tumor_205

source_name: NPC (PSA-NCAM positive)-derived tumor


title: WT_2c_C1 [libB.C1]


title: rip_input_nxf2

description:
Sample 42
Flies expressing GFP-Nxf2.


title: NCAM-NPC_tumor_180


title: OMM (Outer Mito. Membrane) + Nocodazole 6min Target 1

description:
See protocols section
OMM-noco-6min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt

tag: cell line


title: OMM (Outer Mito. Membrane) + Nocodazole 3min Target 2

description:
See protocols section
OMM-noco-3min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: rip_nxf2

description:
Sample 43
Flies expressing GFP-Nxf2.


title: OMM (Outer Mito. Membrane) + Nocodazole 6min Target 2

description:
See protocols section
OMM-noco-6min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: INI1loss_cancer_cell_GSK_PCI

source_name: hiPSC INI1-/-; TP53-/--derived cancer cell

tag: cell type


title: Sample 41_osc_rna_tether_renilla_k9_comb

description: transfected with rna sensor and lambdaN-Renilla

data_processing:
RNA-seq, small RNA-seq and ChIP-seq analysis
Raw fastq files generated by Illumina sequencing were analysed by a pipeline developed in-house. In short, the first and last base of each 50 bp read were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). High-quality reads were aligned to the Drosophila melanogaster genome release 6 (dm6) downloaded from Flybase using STAR. For transposon-wide analysis, genome multi-mapping reads were randomly assigned to one location using option '--outFilterMultimapNmax 1000 --outMultimapperOrder Random' and non-mapping reads were removed. Alignment files were then converted back to fastq format with samtools and re-aligned to the transposon consensus sequences allowing multi-mappers that were assigned to a random position. Generated bam alignment files were indexed using samtools index. For genome-wide analyses, multi-mapping reads were removed to ensure unique locations of reads.
Normalization was achieved by calculating rpm (reads per million) using the deepTools2 bamCoverage function with 10 bp bin sizes. A scaling factor was applied for transposon alignment files, which was calculated by the ratio of reads that aligned to transposon consensus sequences and genome aligned reads. Reads mapping to genes were counted with htseq and transposon derived reads were calculated using a custom script. Metaplots flanking euchromatic insertion sites and transposon coverage plots were calculated by deepTools2 with bin sizes of 10 bp and 50 bp, respectively. Stranded RNA libraries were trimmed, aligned and indexed as described above. Alignment files were split in sense and antisense reads using samtools view. Normalization was performed as described above. For transposon expression analysis only sense reads were considered. Differential expression analysis was performed using custom build R scripts. Adapters from raw small RNA fastq files were clipped with fastx_clipper (adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) keeping only reads with at least 23 bp length. Then the first and last 4 bases were trimmed using seqtk (https://github.com/lh3/seqtk). Alignment and normalization were performed as described above. Only high-quality small RNA reads with a length between 23 and 29 bp were used for further analysis of piRNA profiles.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files for all dm6 alignement files, normalized to rpm. For RNA- and smallRNA-seq, sequences were split in sense- and antisense-mapping reads before normalization.

source_name: ovarian somatic cells (OSC)

growth_protocol:
For samples 1-24,37-41: Flies and cells were grown at 25°C
For samples 25-32: Flies and cells were grown at 25°C
For samples 33-36: Flies were grown at 25°C

extract_protocol:
For samples 1-24,37-41: Samples were crosslinked in formaldehyde and lysed, followed by sonication.
For samples 25-32: OSCs were resuspended in Trizol, flies homogenized in Trizol. RNA was isolated using RNeasy mini prep column (Qiagen).
For samples 33-36: Flies were homogenized in Trizol and RNA extracted using Phenol/Chloroform
For samples 1-24,37-41: NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
For samples 25-32: NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)
For samples 33-36: Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.

treatment_protocol:
For samples 1-24,37-41: OSCs were treated with siRNA or transfected with indicated plasmids
For samples 25-32: OSCs were treated with siRNA or transfected with indicated plasmids

value: OSC

value: ovarian somatic cells (OSC)

tag: chip antibody

value: anti-H3K9me3 (Active Motif #39161)


title: Sample 40_osc_rna_tether_piwi_k9_comb

description: transfected with rna sensor and lambdaN-Piwi


title: OMM (Outer Mito. Membrane) + Nocodazole 3min Target 1

description:
See protocols section
OMM-noco-3min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt

tag: protocol


title: WT_MII_B6 [libB.B6]

value: MII


title: control_differentiation #1

value: ES-cell derived A2 lox.Cre Bcl6 progenitor cells

tag: treatment

value: DMSO

value: day 12


title: WT_MII_B7 [libB.B7]


title: INI1loss_cancer_cell_PCI

tag: analysis method


title: NES (Cytosol) + Nocodazole 30min Control 1

description:
See protocols section
NES-noco-30min-C1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt

value: APEX-seq

tag: cell compartment

value: cytosol


title: Sample 39_osc_rna_tether_panx_k9_comb

description: transfected with rna sensor and lambdaN-Panx


title: WT_MII_B5 [libB.B5]


title: INI1loss_cancer_cell_GSK


title: Sample 38_osc_rna_tether_nxt1_k9_comb

description: transfected with rna sensor and lambdaN-Nxt1


title: NCAM-NPC_tumor_206


title: OMM (Outer Mito. Membrane) + Nocodazole 9min Target 1

description:
See protocols section
OMM-noco-9min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt

value: Outer Mitochondrial Membrane


title: NES (Cytosol) + Nocodazole 3min Control 2

description:
See protocols section
NES-noco-3min-C2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: Sample 37_osc_rna_tether_nxf2_k9_comb

description: transfected with rna sensor and lambdaN-Nxf2


title: WT_MII_B8 [libB.B8]


title: WT_MII_B4 [libB.B4]


title: INI1loss_cancer_cell_DMSO


title: WT_MII_B2 [libB.B2]


title: HPC7_EV_H3K4me1_rep1

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Subread with settings -t 1 (DNA alignment mode)
Snai1 peaks were called using MACS2 with setting --nomodel
H3K4me1/2 reads were quantified +/- 5kb TSS using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak file for Snai1 peaks, txt for H3K4me1/2 count summaries

source_name: HPC7 cells

growth_protocol: HPC7 cells were cultured in vitro in RPMI supplemented with 0.05mM 2-mercaptoethanol, 10% FCS and 100ng/ml mSCF

extract_protocol:
Cells were sorted for GFP expression one week after viral transduction and expanded for ChIP-sequencing. Cells were fixed in 1% formaldehyde for 10 minutes at room temperature. To terminate cross linking 0.125M glycine was added for 5 minutes, washed with PBS and lysed (10mM Tris, 10mM NaCl, 0.2% NP-40) on ice for 10 minutes. Pelleted nuclei were then lysed in nucleus lysis buffer (50mM Tris, 10mM EDTA, 150mM NaCl, 1% Triton-X100, 0.01% SDS) and DNA sonicated to yield an average fragmentation size of 200bp. Sonicated chromatin was pre-cleared with rabbit IgG and immunoprecipitated with antibody and protein G beads. Immunoprecipitated chromatin was eluted using Elution Buffer (100mM NaHCO3, 1%SDS) and reverse cross linked by incubation with RNAse A and 0.3M NaCl, followed by incubation with Proteinase K. Purified DNA was re-suspended in 20ul nuclease-free water for sequencing.
ChIP-sequencing libraries were prepared using the Truseq ChIP library preparation kit from Illumina (Snai1 ChIP) or a variation of Illumina's standard protocol by BGI (H3K4me1 and H3K4me2).

treatment_protocol: HCP7 cells were retrovirally transduced with a MSCV-IRES-GFP vector containing either no gene (MIG-0), wild-type Snai1 (MIG-wt) or mutant Snai1 (MIG-MUT) cDNA. The Snai1 mutant cDNA encodes a mutant protein with a F>A amino acid substitution at position 5 of the protein. This mutation impairs Snai1's ability to interact with the Lsd1 protein.

tag: tissue

value: HPC7 cells

value: empty vector


title: HPC7_EV_H3K4me2_rep1


title: WT_MII_B3 [libB.B3]


title: Sample 36_ovary_panx_hom_smallrna_rep1

description: Panx [M1/M4] KO

growth_protocol:
For samples 1-32: Flies and cells were grown at 25°C
For samples 33-36: Flies were grown at 25°C

extract_protocol:
For samples 1-24: Samples were crosslinked in formaldehyde and lysed, followed by sonication.
For samples 25-32: OSCs were resuspended in Trizol, flies homogenized in Trizol. RNA was isolated using RNeasy mini prep column (Qiagen).
For samples 33-36: Flies were homogenized in Trizol and RNA extracted using Phenol/Chloroform
For samples 1-24: NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
For samples 25-32: NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)
For samples 33-36: Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.

treatment_protocol: For samples 1-32: OSCs were treated with siRNA or transfected with indicated plasmids

value: Panx [M1/M4] KO


title: Sample 35_ovary_panx_het_smallrna_rep1

description: Panx het KO

value: Panx het KO


title: WT_MII_B1 [libB.B1]

value: WT


title: NES (Cytosol) + Nocodazole 30min Control 2

description:
See protocols section
NES-noco-30min-C2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: Sample 34_ovary_nxf2_hom_smallrna_rep1

description: Nxf2 [delta1/F10] KO

value: ovary

value: Nxf2 [delta1/F10] KO


title: HPC7_mut_H3K4me2_rep1

value: mutant version of Snai1


title: KO_MII_A8 [libB.A8]

value: Plag1 knockout


title: Sample 33_ovary_nxf2_het_smallrna_rep1

description: Nxf2 het KO

value: Nxf2 het KO


title: HPC7_mut_H3K4me1_rep1


title: NES (Cytosol) + Nocodazole 30min Target 2

description:
See protocols section
NES-noco-30min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: NES (Cytosol) + Nocodazole 3min Control 1

description:
See protocols section
NES-noco-3min-C1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: KO_MII_A7 [libB.A7]

value: MII


title: Sample 32_panx_hom_ovary_rna_comb

description: Panx [M1/M4] KO


title: KO_MII_A6 [libB.A6]


title: NES (Cytosol) + Nocodazole 9min Target 2

description:
See protocols section
NES-noco-9min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: HPC7_WT_H3K4me2_rep1

value: wildtype Snai1


title: HPC7_WT_H3K4me1_rep1


title: NES (Cytosol) + Nocodazole 9min Target 1

description:
See protocols section
NES-noco-9min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: HPC7_WT_IgG_rep1


title: NES (Cytosol) + Nocodazole 2hr Target 2

description:
See protocols section
NES-noco-2hr-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: Sample 31_panx_het_ovary_rna_comb

description: Panx het KO


title: NES (Cytosol) + Nocodazole 30min Target 1

description:
See protocols section
NES-noco-30min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: NES (Cytosol) + Nocodazole 6min Target 2

description:
See protocols section
NES-noco-6min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: KO_MII_A5 [libB.A5]


title: Sample 30_nxf2_hom_ovary_rna_comb

description: Nxf2 [delta1/F10] KO


title: HPC7_WT_IgG_rep2


title: NES (Cytosol) + Nocodazole 2hr Target 1

description:
See protocols section
NES-noco-2hr-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: HPC7_EV_H3K4me2_rep3


title: KO_MII_A4 [libB.A4]


title: KO_MII_A3 [libB.A3]


title: NES (Cytosol) + Nocodazole 6min Target 1

description:
See protocols section
NES-noco-6min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: NES (Cytosol) + Nocodazole 3min Target 2

description:
See protocols section
NES-noco-3min-T2
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: KO_MII_A2 [libB.A2]


title: HPC7_EV_H3K4me2_rep2


title: NES (Cytosol) + Nocodazole 3min Target 1

description:
See protocols section
NES-noco-3min-T1
processed data files:
APEX_seq_counts_omm_nes_nocodazole_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_nocodazole_polyA_hek293t.txt


title: KO_MII_A1 [libB.A1]


title: HPC7_mut_H3K4me2_rep3


title: Sample 27_osc_sipanx_rna_comb

description: Panx knockdown

value: OSC

value: ovarian somatic cells (OSC)

value: Panx knockdown


title: Cytosol Fractionation 2

description:
Cyto-frac-2
processed data files:
Fractionation_counts_polyA_hek293t.txt

growth_protocol: HEK 293T cells from the ATCC (passages < 25) were cultured in a 1:1 DMEM/MEM mixture (Cellgro) supplemented with 10% fetal bovine serum, 50 units/mL penicillin, and 50 mg/mL streptomycin at 37oC under 5% CO2

extract_protocol: To validate the NLS APEX-seq data we carried out nuclear fractionation of HEK 293T cells by following an established protocol (Gagnon et al., Nature Protocols 2014). We modified the protocol so that the extracted RNA was not purified by trizol extraction, but rather by using the RNeasy plus mini kit (Qiagen). RNA-seq was carried out using the same protocol as that used for APEX-seq, thereby generating polyA-selected libraries for the nuclear and cytoplasmic fraction using Illumina TruSeq kit.

treatment_protocol: 18-24 hrs after plating HEK 293T cells stably expressing the corresponding APEX2 fusion construct, APEX labeling was initiated by changing the medium to fresh medium containing 500 mM biotin-phenol (Iris Biotech GMBH). This was incubated at 37oC under 5% CO2 for 30 min. H2O2 (Sigma Aldrich) was then added to each well to a final concentration of 1 mM, and the plate gently agitated for 1 min (Rhee et al., Science 2013). The reaction was quenched by replacing the medium with an equal volume of 5 mM Trolox, 10 mM sodium ascorbate and 10 mM sodium azide in Dulbecco's phosphate-buffered saline (DPBS). Cells were washed with DPBS containing 5 mM Trolox and 10 mM sodium ascorbate three times before proceeding to imaging, RT-qPCR or RNA-seq experiments. The unlabeled controls were processed identically, except that the H2O2 addition step was omitted.

value: Fractionation RNA-seq

value: Cytosol fraction


title: Cytosol Fractionation 1

description:
Cyto-frac-1
processed data files:
Fractionation_counts_polyA_hek293t.txt


title: Sample 25_osc_sigfp_rna_comb

description: GFP knockdown

value: GFP knockdown


title: Sample 26_osc_sinxf2_rna_comb

description: Nxf2 knockdown

value: Nxf2 knockdown


title: Nuclear Fractionation 2

description:
Nuc-frac-2
processed data files:
Fractionation_counts_polyA_hek293t.txt

value: Nuclear fraction


title: KO_8c_F7 [libA.F7]


title: HPC7_mut_H3K4me2_rep2

value: HPC7 cells


title: Sample 24_panx_hom_ovary_chip_k9_comb

description: Panx [M1/M4] KO

value: Panx [M1/M4] KO

value: anti-H3K9me3 (Active Motif #39161)


title: HPC7_WT_H3K4me2_rep3


title: HPC7_WT_H3K4me2_rep2


title: KO_8c_F6 [libA.F6]


title: Sample 23_panx_het_ovary_chip_k9_comb

description: Panx het KO

value: ovary

value: Panx het KO


title: KO_8c_F5 [libA.F5]

value: Plag1 knockout


title: Sample 28_osc_sipiwi_rna_comb

description: Piwi knockdown

value: Piwi knockdown


title: HPC7_EV_H3K4me1_rep3

value: empty vector


title: Sample 29_nxf2_het_ovary_rna_comb

description: Nxf2 het KO

value: Nxf2 het KO


title: Sample 22_panx_het_ovary_chip_input

description: Panx het KO


title: Sample 21_osc_sipiwi_k9_comb

description: Piwi knockdown

value: OSC


title: WT_8c_F4 [libA.F4]

value: WT


title: WT_8c_F3 [libA.F3]


title: OMM (Outer Mito. Membrane) +CCCP Control 2

description:
OMM-cccp-C2
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

data_processing:
Library strategy: APEX-seq
The RNA-seq reads were initially subject to barcode removal and primer trimming using a published script (Flynn et al., Nature Protocols 2016) based on Trimmomatic: (https://github.com/qczhang/icSHAPE/blob/master/scripts/trimming.pl): perl trimming.pl -1 $fastq-file1 -2 $fastq-file2 -p $trimmed-file1 -q $trimmed-file2 -l 0 -t 0 -c phred33 -a adapter.fa -m 36
The reads were then mapped using STAR (Dobin et al., Bioinformatics 2013) to the GRCh38 Ensembl genome, with Homo_sapiens.GRCh38.84.gtf annotations (http://uswest.ensembl.org/index.html), using the following command: STAR --genomeDir ~/genome/human/star --runThreadN 8 --readFilesIn $trimmed-file1 $trimmed-file2 --outFileNamePrefix $output-samfile
The mapped reads were then counted using HTSEQ (Anders et al., Bioinformatics 2015) : python -m HTSeq.scripts.count -m intersection-nonempty -s reverse -i gene_id $output-samfile ~/genome/human/Homo_sapiens.GRCh38.84.gtf > $txt
The mapped data was visualized using the UCSC browser track. To generate genome tracks we used samtools to generate stranded BAM files for each library from the SAM file. The BAM file was then used to generate a bedgraph following the command: genomeCoverageBed -bg -split -ibam $bam -g ~/genome/human/star/chrNameLength.txt > $bed_file
Genome_build: hg38
Supplementary_files_format_and_content: Tab-deliminted text files include either DESEQ2 log2foldchanges and Padjusted values; or count data from STAR and HTSEQ. Differentially-expressed genes were determined using DESeq2 (Love et al., Genome Biology 2014), using FDR < 0.05 and 18 controls. All P-values from DESeq2 are FDR adjusted for multiple-hypothesis testing. For the OMM perturbation experiments, we used the same 18-control strategy, but replacing the unperturbed OMM APEX-seq and NES APEX-seq values with the corresponding drug-perturbed values. There were two exceptions to the 18-control approach in all our analysis. For the LMA gene in nuclear lamina, and the SENP2 gene in the nuclear pore construct, the unlabeled control had high counts for these genes in the RNA-seq data, as these genes were used to target APEX to the corresponding location. Therefore, to compensate, we replaced the LMA 18-control DESeq2 log2fold change with the 2-control log2fold change (using LMA controls) in the LMA data; we did the same for SENP2 in the nuclear pore dataset. Otherwise, all other data was as is.

extract_protocol:
To labeled and unlabeled (controls) HEK 293T cells in 10-cm plates, we added ~1 ml DPBS containing 5 mM Trolox and 10 mM sodium ascorbate, as well as ~4 ul Ribolock RNAse inhibitor (Thermo Fischer Scientific). The cells were then scrapped off 10-cm plates using cell lifters (Corning), transferred to 2-ml Eppendorf tubes, and spun at 500G for 4 minutes to pellet cells. The supernatant was removed, and the cells were processed using the RNeasy plus mini kit (Qiagen) following the manufacture protocol, including adding beta-mercaptoethanol to the lysis buffer. The cells were sent through the genomic DNA (gDNA) eliminator column supplied with the kit. One modification to the protocol was replacing the RW1 buffer with RWT buffer (Qiagen) for washing. The extracted RNA was eluted into RNAse-free water, and RNA integrity was checked using the Agilent bioanalyzer 2100 using the “high-sensitivity” setting. Only RNA with a RIN (RNA integrity number) > 8.5 was used for subsequent experiments. RNAs shorter than 100 nt were not efficiently recovered.
RNA Seq libraries were prepared from enriched RNA (corresponding to ~30-50 µg of pre-enriched RNA) using the Illumina TruSeq Stranded mRNA Protocol, which included polyA+ selection. The prepared libraries were stranded and were quality-controlled by sequencing on the Illumina Miseq. Good libraries (> 80% unique reads) were sequenced on the Illumina Hiseq400 at ~35 million paired (2 x 75) reads per library. The correlation between biological replicates was high (between 0.96 and 1). For the MITO APEX Seq we also generated total RNA samples (by omitting the polyA+ selection step in the TruSeq protocol), as well as a polyA+ selected technical replicate for 1 of the labeled samples.

value: APEX-seq

value: Outer Mitochondrial Membrane


title: HPC7_EV_H3K4me1_rep2


title: HPC7_mut_H3K4me1_rep3

value: mutant version of Snai1


title: OMM (Outer Mito. Membrane) +CCCP Target 2

description:
OMM-cccp-T2
processed data files:
Omm_cccp_targets_fwd.norm_avg.bw
Omm_cccp_targets_rev.norm_avg.bw
Omm_cccp_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: OMM (Outer Mito. Membrane) +CCCP Control 1

description:
OMM-cccp-C1
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: Sample 20_osc_sipiwi_k4_comb

description: Piwi knockdown

value: ovarian somatic cells (OSC)

value: anti-H3K4me2 (Millipore # 07-030)


title: WT_8c_F2 [libA.F2]


title: HPC7_mut_H3K4me1_rep2


title: KO_8c_F8 [libA.F8]


title: Nuclear Fractionation 1

description:
Nuc-frac-1
processed data files:
Fractionation_counts_polyA_hek293t.txt

value: Fractionation RNA-seq

value: Nuclear fraction


title: OMM (Outer Mito. Membrane) +CCCP Target 1

description:
OMM-cccp-T1
processed data files:
Omm_cccp_targets_fwd.norm_avg.bw
Omm_cccp_targets_rev.norm_avg.bw
Omm_cccp_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: Sample 18_osc_sipanx_k4_comb

description: Panx knockdown

value: Panx knockdown


title: KO_8c_E7 [libA.E7]


title: KO_8c_E6 [libA.E6]


title: HPC7_WT_H3K4me1_rep3

value: HPC7 cells

value: wildtype Snai1


title: NES (Cytosol) +CCCP Control 2

description:
NES-cccp-C2
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: Cytosol


title: Sample 17_osc_sinxf2_k9_comb

description: Nxf2 knockdown

value: Nxf2 knockdown

value: anti-H3K9me3 (Active Motif #39161)


title: NES (Cytosol) +CCCP Target 2

description:
NES-cccp-T2
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: HPC7_WT_H3K4me1_rep2


title: HPC7 Snai1 MUT Snai1 ChIP - technical rep 4


title: KO_8c_E8 [libA.E8]

value: Plag1 knockout


title: NES (Cytosol) +CCCP Control 1

description:
NES-cccp-C1
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: Sample 15_osc_sigfp_k9_comb

description: GFP knockdown

value: GFP knockdown


title: KO_8c_E5 [libA.E5]


title: HPC7 Snai1 MUT Snai1 ChIP - technical rep 3


title: NES (Cytosol) +CCCP Target 1

description:
NES-cccp-T1
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: WT_8c_E4 [libA.E4]


title: Sample 16_osc_sinxf2_k4_comb

description: Nxf2 knockdown

value: OSC


title: HPC7 Snai1 MUT Snai1 ChIP - technical rep 2


title: OMM (Outer Mito. Membrane) +Puromycin Control 2

description:
OMM-puro-C2
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: WT_8c_E3 [libA.E3]

value: WT


title: HPC7 Snai1 MUT Snai1 ChIP - technical rep 1


title: OMM (Outer Mito. Membrane) +Puromycin Control 1

description:
OMM-puro-C1
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: APEX-seq


title: Sample 13_osc_dna_tether_renilla_k9_comb

description: transfected with dna sensor and LacI-Renilla


title: Sample 12_osc_dna_tether_renilla_k4_comb

value: transfected with dna sensor and LacI-Renilla


title: HPC7 EV Snai1 ChIP - technical rep 4

value: empty vector


title: Sample 19_osc_sipanx_k9_comb

description: Panx knockdown

value: ovarian somatic cells (OSC)


title: WT_8c_E1 [libA.E1]


title: HPC7 EV Snai1 ChIP - technical rep 3


title: OMM (Outer Mito. Membrane) +Puromycin Target 2

description:
OMM-puro-T2
processed data files:
Omm_puro_targets_fwd.norm_avg.bw
Omm_puro_targets_rev.norm_avg.bw
Omm_puro_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: Outer Mitochondrial Membrane


title: HPC7 EV Snai1 ChIP - technical rep 2


title: Sample 11_osc_dna_tether_piwi_k9_comb

description: transfected with dna sensor and LacI-Piwi


title: KO_2c_D8 [libA.D8]


title: OMM (Outer Mito. Membrane) +Puromycin Target 1

description:
OMM-puro-T1
processed data files:
Omm_puro_targets_fwd.norm_avg.bw
Omm_puro_targets_rev.norm_avg.bw
Omm_puro_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: Sample 14_osc_sigfp_k4_comb

description: GFP knockdown

value: anti-H3K4me2 (Millipore # 07-030)


title: KO_2c_D7 [libA.D7]


title: Sample 10_osc_dna_tether_piwi_k4_comb

value: transfected with dna sensor and LacI-Piwi


title: KO_2c_D6 [libA.D6]


title: HPC7 EV Snai1 ChIP - technical rep 1


title: NES (Cytosol) +Puromycin Control 1

description:
NES-puro-C1
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: NES (Cytosol) +Puromycin Control 2

description:
NES-puro-C2
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: Sample 9_osc_dna_tether_panx_k9_comb

description: transfected with dna sensor and LacI-Panx


title: HPC7 Snai1 MUT input - technical rep 3

value: mutant version of Snai1


title: WT_2c_D5 [libA.D5]


title: Sample 8_osc_dna_tether_panx_k4_comb

value: transfected with dna sensor and LacI-Panx


title: NES (Cytosol) +Puromycin Target 1

description:
NES-puro-T1
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: NES (Cytosol) +Puromycin Target 2

description:
NES-puro-T2
processed data files:
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: WT_2c_D4 [libA.D4]


title: WT_8c_E2 [libA.E2]


title: HPC7 Snai1 MUT input  - technical rep 2

value: HPC7 cells


title: Sample 6_osc_dna_tether_nxf2_k4_comb

description: transfected with dna sensor and LacI-Nxf2


title: KO_2c_D3 [libA.D3]


title: Sample 5_osc_dna_tether_hp1_k9_comb

description: transfected with dna sensor and LacI-HP1a


title: OMM (Outer Mito. Membrane) +Cycloheximide Control 2

description:
OMM-cyc-C2
processed data files:
Omm_cyc_controls_fwd.norm_avg.bw
Omm_cyc_controls_rev.norm_avg.bw
Omm_cyc_controls_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: OMM (Outer Mito. Membrane) +Cycloheximide Control 1

description:
OMM-cyc-C1
processed data files:
Omm_cyc_controls_fwd.norm_avg.bw
Omm_cyc_controls_rev.norm_avg.bw
Omm_cyc_controls_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: KO_2c_D2 [libA.D2]


title: HPC7 Snai1 MUT input - technical rep 4


title: HPC7 EV input - technical rep 4


title: Sample 7_osc_dna_tether_nxf2_k9_comb

value: transfected with dna sensor and LacI-Nxf2


title: OMM (Outer Mito. Membrane) +Cycloheximide Target 2

description:
OMM-cyc-T2
processed data files:
Omm_cyc_targets_fwd.norm_avg.bw
Omm_cyc_targets_rev.norm_avg.bw
Omm_cyc_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: Sample 4_osc_dna_tether_hp1_k4_comb

value: transfected with dna sensor and LacI-HP1a


title: HPC7 EV input - technical rep 3


title: Sample 3_nxf2_hom_ovary_chip_k9_comb

description: Nxf2 [delta1/F10] KO

value: ovary

value: Nxf2 [delta1/F10] KO

value: anti-H3K9me3 (Active Motif #39161)


title: KO_2c_D1 [libA.D1]

value: Plag1 knockout


title: NES (Cytosol) +Cycloheximide Control 2

description:
NES-cyc-C2
processed data files:
Nes_cyc_controls_fwd.norm_avg.bw
Nes_cyc_controls_rev.norm_avg.bw
Nes_cyc_controls_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: Cytosol


title: WT_2c_C4 [libA.C4]

value: WT


title: WT_2c_C3 [libA.C3]


title: OMM (Outer Mito. Membrane) +Cycloheximide Target 1

description:
OMM-cyc-T1
processed data files:
Omm_cyc_targets_fwd.norm_avg.bw
Omm_cyc_targets_rev.norm_avg.bw
Omm_cyc_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: APEX-seq


title: HPC7 EV input - technical rep 2

value: empty vector


title: HPC7 EV input  - technical rep 1


title: HPC7 Snai1 MUT input - technical rep 1


title: WT_2c_C2 [libA.C2]


title: Sample 2_nxf2_het_ovary_chip_k9_comb

description: Nxf2 het KO

value: Nxf2 het KO


title: NES (Cytosol) +Cycloheximide Target 2

description:
NES-cyc-T2
processed data files:
Nes_cyc_targets_fwd.norm_avg.bw
Nes_cyc_targets_rev.norm_avg.bw
Nes_cyc_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: HPC7 Snai1WT Snai1 ChIP - technical rep 3

value: wildtype Snai1


title: HPC7 Snai1WT Snai1 ChIP - technical rep 4


title: WT_2c_C1 [libA.C1]


title: KO_MII_B8 [libA.B8]

value: MII


title: HPC7 Snai1WT Snai1 ChIP - technical rep 2


title: Sample 1_nxf2_het_ovary_chip_input

description: Nxf2 het KO


title: NES (Cytosol) +Cycloheximide Control 1

description:
NES-cyc-C1
processed data files:
Nes_cyc_controls_fwd.norm_avg.bw
Nes_cyc_controls_rev.norm_avg.bw
Nes_cyc_controls_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: NES (Cytosol) +Cycloheximide Target 1

description:
NES-cyc-T1
processed data files:
Nes_cyc_targets_fwd.norm_avg.bw
Nes_cyc_targets_rev.norm_avg.bw
Nes_cyc_targets_sorted.norm_avg.bw
APEX_seq_counts_omm_nes_drug_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: MITO (Mitochondrial Matrix) Control 2 total

description:
MITO-Tot-C2
processed data files:
APEX_seq_counts_mito_data_hek293t.txt

value: Mitochondrial Matrix


title: KO_MII_B7 [libA.B7]


title: HPC7 Snai1WT Snai1 ChIP - technical rep 1


title: MITO (Mitochondrial Matrix) Control 1 total

description:
MITO-Tot-C1
processed data files:
APEX_seq_counts_mito_data_hek293t.txt


title: MITO (Mitochondrial Matrix) Target 2 total

description:
MITO-Tot-T2
processed data files:
APEX_seq_counts_mito_data_hek293t.txt


title: HPC7 Snai1WT input - technical rep 3


title: MITO (Mitochondrial Matrix) Target 1 total

description:
MITO-Tot-T1
processed data files:
APEX_seq_counts_mito_data_hek293t.txt


title: HPC7 Snai1WT input - technical rep 4


title: KO_MII_B3 [libA.B3]


title: HPC7 Snai1WT input - technical rep 1


title: KO_MII_B4 [libA.B4]


title: KO_MII_B6 [libA.B6]


title: HPC7 Snai1WT input - technical rep 2


title: KO_MII_B5 [libA.B5]


title: KO_MII_B2 [libA.B2]


title: MITO (Mitochondrial Matrix) Control 2 polyA

description:
MITO-C2
processed data files:
Mito_controls_fwd.norm_avg.bw
Mito_controls_rev.norm_avg.bw
Mito_controls_sorted.norm_avg.bw
APEX_seq_counts_mito_data_hek293t.txt
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: 4d red light grown rcb-10 seedlings/replicate 1

city: Riverside

first: MENG

last: Chen

state: CALIFORNIA

address: 900 University Ave, 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: UC Riverside

description: Gene expression data from 4-d-old rcb-10 grown in 10 μmol m-2 s-1 R light

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: GeneSpring GX 12.1 to RMA normalize and correct background on all the data

organism: Arabidopsis thaliana

source_name: whole seedling (root, hypocotyl, cotyledon)

label_protocol: Standard Affymetrix procedures

growth_protocol: Wild-type (Col-0) and rcb-10 mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. After 4 days of stratification in the dark at 4ºC, seedlings were grown in 10 μmol m-2 s-1 R light.

extract_protocol: Total RNA was extracted using SpectrumTM Plant Total RNA kit (Sigma)

tag: ecotype


title: ES_WT_D0_2_T_4C

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: CRG

data_processing:
Library strategy: UMI-4C seq
(RNAseq) RNAseq was aligned with STAR and genome annotation Gencode M17.
(RNAseq) Annotation was done using STAR --genecounts option.
(UMI-4C) Split fastq files at restriction enzyme (RE) sites, producing the corresponding fragments
(UMI-4C) Alignment using bwa mem and default options
(UMI-4C) Remove supplementary and low mapping quality (< 20) alignments
(UMI-4C) Annotate pair reads as specific if there is a RE site in the first read
(UMI-4C) Annotate pair reads as mapped if at least one fragment (besides the first one) is properly aligned
(UMI-4C) Keep only read pairs that are specific, mapped and not duplicated (same alignment positions for all its fragments)
Genome_build: mm10
Supplementary_files_format_and_content: (RNAseq) bigwig files were generated with deeptools, (UMI-4C) txt processed files

source_name: ESCs

growth_protocol: Mouse ESCs were cultured on plastic dishes pre-coated with 0.1% (W/V) EmbryoMax® gelatine (EMD Millipore) with either DMEM/F12 medium and Neurobasal® medium mixed at 1:1 ratio, supplemented with MEM non-essential amino acids solution (1X), sodium pyruvate (1mM), L-glutamine (2mM), Penicillin (100 U/mL), Streptomycin (100μg/mL), beta-mercaptoethanol (ME, 50μM), N2 and B27 supplements, the small-molecule inhibitors PD0325901 (1μM, Selleck Chemicals) and CHIR99021 (3 μM, Selleck Chemicals), and ESGRO® Leukaemia Inhibitory Factor (LIF) (1000 U/mL, EMD Millipore), or with KnockoutTM DMEM medium supplemented with 15% (V/V) ES cell qualified foetal bovine serum (ES FBS), MEM non-essential amino acids (1X), sodium pyruvate (1mM), L-glutamine (2mM), Penicillin (100 U/mL), Streptomycin (100μg/mL) and 50μM ME.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. UMI-4C libraries were purified with AmpureXP beads.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA library Preparation Kit. UMI-4C libraries were prepared according stardard NEBNext DNA libaray preparation instructions.

treatment_protocol: ESCs was induced to form EBs with “EB differentiation medium” (KnockoutTM DMEM medium supplemented with 10% FBS, MEM non-essential amino acids (1X), sodium pyruvate (1mM), L-glutamine (2mM), Penicillin (100 U/mL), Streptomycin (100μg/mL) and 50μM ME and plated as hanging drops (400 cells in 20μL) on the lid of a 100 mm Petri dish. The cultures were harvested 3 days later and transferred into bacterial dishes for further culture in suspension.

value: wild type

value: ESCs

tag: passages

value: Day 0

tag: group

value: T 4C tag


title: 4d red light grown rcb-10 seedlings/replicate 3

tag: genotype


title: 4d red light grown rcb-10 seedlings/replicate 2


title: 4d red light growth WT (Col-0) seedlings/replicate 3

description: Gene expression data from 4-d-old Col-0 grown in 10 μmol m-2 s-1 R light


title: MITO (Mitochondrial Matrix) Target 2 Technical Replicate

description:
MITO-Rep-T2
processed data files:
APEX_seq_counts_mito_data_hek293t.txt


title: KO_MII_B1 [libA.B1]


title: dcp5_SS_L4h_rep3

city: Taipei

first: Geng-Jen

last: Jang

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16.5 hr at 45°C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GeneChip Operating System 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The value of polysome-bound RNAs is normalized to PL% (the ratio of polysome-bound RNAs in total RNA).

source_name: 4-d-old dcp5-1, L4h

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 300 ng total RNA (MessageAmp Premier RNA Amplification Kit Manual, 4386269 Rev. G, Life Technologies Corporation).Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seeds were surface-sterilized and germinated on half-strength Murashige and Skoog

extract_protocol: Total RNA and polysome-bound RNA were extracted as described previously [(Liu et al, Mol Syst Biol 8, 566 (2012)]

treatment_protocol: 4-d-old etiolated seedlings treated with or without 4-h white light

value: seedlings (aerial parts)

value: white light

tag: rna fraction

value: total RNA


title: dcp5_SS_Dark_rep3

source_name: 4-d-old dcp5-1, Dark

value: dark


title: ES_WT_D0_2_Gata6_4C

value: Gata6 4C tag


title: 4d red light growth WT (Col-0) seedlings/replicate 1


title: 4d red light growth WT (Col-0) seedlings/replicate 2


title: MITO (Mitochondrial Matrix) Target 2 polyA

description:
MITO-T2
processed data files:
Mito_targets_fwd.norm_avg.bw
Mito_targets_rev.norm_avg.bw
Mito_targets_sorted.norm_avg.bw
APEX_seq_counts_mito_data_hek293t.txt
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: WT_MII_A8 [libA.A8]


title: WT_SS_L4h_rep3

source_name: 4-d-old Col-0, L4h

value: control


title: MITO (Mitochondrial Matrix) Control 1 polyA

description:
MITO-C1
processed data files:
Mito_controls_fwd.norm_avg.bw
Mito_controls_rev.norm_avg.bw
Mito_controls_sorted.norm_avg.bw
APEX_seq_counts_mito_data_hek293t.txt
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: ES_WT_D0_2_Gata4_4C

value: Gata4 4C tag


title: ES_WT_D0_2_Foxa2_4C

value: Foxa2 4C tag


title: WT_MII_A7 [libA.A7]

value: WT


title: ES_WT_D0_1_T_4C


title: WT_MII_A5 [libA.A5]


title: WT_SS_Dark_rep3

source_name: 4-d-old Col-0, Dark


title: WT_MII_A6 [libA.A6]


title: OMM (Outer Mito. Membrane) Control 2

description:
OMM-C2
processed data files:
Omm_controls_fwd.norm_avg.bw
Omm_controls_rev.norm_avg.bw
Omm_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: APEX-seq

value: Outer Mitochondrial Membrane


title: ES_WT_D0_1_Gata6_4C


title: ES_WT_D0_1_Gata4_4C


title: WT_MII_A4 [libA.A4]

value: MII


title: OMM (Outer Mito. Membrane) Target 2

description:
OMM-T2
processed data files:
Omm_targets_fwd.norm_avg.bw
Omm_targets_rev.norm_avg.bw
Omm_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: WT_MII_A3 [libA.A3]


title: dcp5_PL_Dark_rep3

value: polysome-bound RNA


title: dcp5_PL_L4h_rep3


title: OMM (Outer Mito. Membrane) Target 1

description:
OMM-T1
processed data files:
Omm_targets_fwd.norm_avg.bw
Omm_targets_rev.norm_avg.bw
Omm_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: WT_PL_L4h_rep3


title: MITO (Mitochondrial Matrix) Target 1 polyA

description:
MITO-T1
processed data files:
Mito_targets_fwd.norm_avg.bw
Mito_targets_rev.norm_avg.bw
Mito_targets_sorted.norm_avg.bw
APEX_seq_counts_mito_data_hek293t.txt
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt

value: Mitochondrial Matrix


title: ES_WT_D0_1_Foxa2_4C

value: wild type

value: ESCs


title: WT_PL_Dark_rep3


title: KDEL (ER Lumen) Control 2

description:
KDEL-C2
processed data files:
Kdel_controls_fwd.norm_avg.bw
Kdel_controls_rev.norm_avg.bw
Kdel_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: ER Lumen


title: ES_KO_D0_2_T_4C

value: Day 0

value: T 4C tag


title: WT_MII_A2 [libA.A2]


title: OMM (Outer Mito. Membrane) Control 1

description:
OMM-C1
processed data files:
Omm_controls_fwd.norm_avg.bw
Omm_controls_rev.norm_avg.bw
Omm_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: KDEL (ER Lumen) Control 1

description:
KDEL-C1
processed data files:
Kdel_controls_fwd.norm_avg.bw
Kdel_controls_rev.norm_avg.bw
Kdel_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: ES_KO_D0_2_Gata6_4C


title: KDEL (ER Lumen) Target 2

description:
KDEL-T2
processed data files:
Kdel_targets_fwd.norm_avg.bw
Kdel_targets_rev.norm_avg.bw
Kdel_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: endo_KO_14

data_processing:
The libraries were sequenced by two lanes of Illumina HiSeq2000 instrument. The sequenced raw STRT reads were processed by STRTprep [PMID: 26874359]; v3dev branch, d7efcde commit (https://github.com/shka/STRTprep/tree/v3dev) to demultiplex according to the barcode, and to exclude redundant reads according to the UMI; sequence of the template switching oligo (UMI, barcode and tri-G) were trimmed.
A gft file comprising annotations retrieved from UCSC and the ERCC annotations, was used to estimate the reads in all annotated genes using htseq-count.
Genome_build: Mm9
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts of annotated genes and ERCC controls

source_name: Uterus

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen, Hilden, Germany) and quality measured with the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA). Ten nanograms of high-quality RNA (RIN>8) was used for RNA-seq.
One 46-plex STRT RNA-seq library was made using 10 ng RNA as described previously (Krjutskov et al. 2016 Hum Reprod 31:844) with the following modifications: barcoded 10 µM template-switching oligonucleotides were added prior to reverse transcriptase, ERCC spike-in Mix A was diluted 15,300-fold with clean water, and 1 µl was taken per library reverse transcriptase master mix. Twenty cycles of PCR were used for the first round of amplification and ten additional cycles for the second round to introduce Illumina-compatible universal sequences.

treatment_protocol: Sexually mature Plag1KO and WT females were superovulated by i.p. injections of 5 IU pregnant mare serum (Folligon; Intervet, Dublin, Ireland), followed two days later by 5 IU human chorionic gonadotropin (hCG) (Chorulon; Intervet, Dublin, Ireland). The following day the animals were killed and uteri removed.

value: endometrium

tag: mouse id


title: WT_MII_A1 [libA.A1]

extract_protocol:
No extraction.
Single embryos or uncultured oocytes were picked into 4 ml library lysis buffer containing 5 mM Tris-HCl pH 8.0 (Sigma-Aldrich), 2 mM dNTP mixture (ThermoFisher Scientific, Waltham, MA, USA), 10 mM DTT (Sigma-Aldrich), 0.05% Triton X-100 (Sigma-Aldrich), 400 nM anchored oligo(dT) primer biotin-TTAAGCAGTGGTATCAACGCAGAGTCGAC(T)29V where V is LNA nucleotide (Exiqon, Vedbaek, Denmark), and 4 U RiboLock RNase inhibitor (ThermoFisher). Two separate 46-plex libraries (libA and libB) were made as described previously (Krjutskov et al. 2016 Hum Reprod 31:844) with the following modifications: barcoded 10 µM template-switching oligonucleotides were added prior to reverse transcriptase, ERCC spike-in Mix A was diluted 15,300-fold with clean water, and 1 µl was taken per library reverse transcriptase master mix. Twenty cycles of PCR were used for the first round of amplification and ten additional cycles for the second round to introduce Illumina-compatible universal sequences. Both libraries contained all developmental stages and genotypes.


title: dcp5_SS_L4h_rep2

value: seedlings (aerial parts)

value: white light

value: total RNA


title: ES_KO_D0_2_Gata4_4C

value: Gata4 4C tag


title: KDEL (ER Lumen) Target 1

description:
KDEL-T1
processed data files:
Kdel_targets_fwd.norm_avg.bw
Kdel_targets_rev.norm_avg.bw
Kdel_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: ERM (ER Membrane) Control 2

description:
ERM-C2
processed data files:
Erm_controls_fwd.norm_avg.bw
Erm_controls_rev.norm_avg.bw
Erm_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: ER Membrane


title: endo_KO_13


title: WT_SS_L4h_rep2

value: control


title: myo_WT_12 [F6]

value: WT

value: myometrium


title: ES_KO_D0_1_T_4C


title: dcp5_SS_Dark_rep2

value: dark


title: ES_KO_D0_1_Gata6_4C

value: Gata6 4C tag


title: endo_WT_12


title: ERM (ER Membrane) Target 2

description:
ERM-T2
processed data files:
Erm_targets_fwd.norm_avg.bw
Erm_targets_rev.norm_avg.bw
Erm_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt

value: APEX-seq


title: endo_KO_11


title: ERM (ER Membrane) Target 1

description:
ERM-T1
processed data files:
Erm_targets_fwd.norm_avg.bw
Erm_targets_rev.norm_avg.bw
Erm_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: endo_WT_10


title: ES_KO_D0_1_Foxa2_4C

value: Foxa2 4C tag


title: dcp5_PL_Dark_rep2

value: polysome-bound RNA


title: dcp5_PL_L4h_rep2


title: WT_PL_L4h_rep2


title: endo_KO_9


title: NES (Cytosol) Control 2

description:
NES-C2
processed data files:
Nes_controls_fwd.norm_avg.bw
Nes_controls_rev.norm_avg.bw
Nes_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: Cytosol


title: EB_WT_D6_2_T_4C

value: wild type

value: embryoid bodies

value: Day 6


title: NES (Cytosol) Control 1

description:
NES-C1
processed data files:
Nes_controls_fwd.norm_avg.bw
Nes_controls_rev.norm_avg.bw
Nes_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt


title: endo_KO_13 [E8]

value: endometrium


title: ES_KO_D0_2_Foxa2_4C

value: ESCs

value: Day 0


title: WT_SS_Dark_rep2

value: seedlings (aerial parts)

value: total RNA


title: dcp5_SS_Dark_rep1


title: EB_WT_D6_2_Gata6_4C


title: dcp5_SS_L4h_rep1

value: white light


title: NES (Cytosol) Target 2

description:
NES-T2
processed data files:
Nes_targets_fwd.norm_avg.bw
Nes_targets_rev.norm_avg.bw
Nes_targets_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt


title: myo_KO_14


title: ERM (ER Membrane) Control 1

description:
ERM-C1
processed data files:
Erm_controls_fwd.norm_avg.bw
Erm_controls_rev.norm_avg.bw
Erm_controls_sorted.norm_avg.bw
APEX_seq_counts_all_data_polyA_hek293t.txt
APEX_seq_deseq2_all_data_polyA_hek293t.txt
APEX_seq_deseq2_omm_nes_drug_polyA_hek293t.txt

value: ER Membrane


title: WT_SS_L4h_rep1

value: control


title: EB_WT_D6_2_Gata4_4C

value: Gata4 4C tag