title: kidney organoid, invivo_4weeks_2

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

institute: Blizard Institute Barts and The London School of Medicine and Dentistry

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to Hg19 human genome using STAR v2.5.2a with parameters --outSAMtype BAM   SortedByCoordinate --outSAMstrandField intronMotif  --outSAMattributes NH   HI   AS   nM   NM   MD --outSAMmapqUnique 50 --outBAMsortingThreadN 16 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFilterType BySJout --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonical --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --quantMode TranscriptomeSAM   GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: Cuffnorm output files with quartile normalized FPKM expression value of each sample replicate.

source_name: Human pluripotent stem cells

growth_protocol: Induction of kidney organoids from human pluripotent stem cells (hPSCs) hPSCs were dissociated into single cells with Accutase (STEMCELL Technologies), and plated onto Matrigel (BD Biosciences)-coated plates at a density of ~15,000 to ~24,000 cells/cm2. The plated cells were cultured in TeSR supplemented with 10 μM Y-27632 (Sigma) for 24 hours, followed by another 48-72 hours culture in TeSR to reach a confluence of 50-60%. To induce primitive streak, cells were cultured in basic differentiation medium (Advanced RPMI 1640, 1x L-GlutaMAX, 1 x NEAA) (Life Technologies) supplemented with 10 μM CHIR99021 (Sigma) for 4 days with daily media change. Next, to induce nephrogenic intermediate mesoderm, cells were cultured in basic differentiation medium, without any growth factor for 3 days with daily media change. Subsequently, to induce nephron progenitors, cells were cultured in basic differentiation media supplemented with 50 ng/mL FGF9 (Peprotech) and 3 μM CHIR99021 with daily media change for 2 days. From day 10 of differentiation onward, cells were cultured in basic differentiation media supplemented with 50 ng/mL FGF9 until day 20. On day 14 of differentiation, cells were pulsed with 1 μM CHIR99021 (patterning CHIR) for 24 hours. From day 20 of differentiation onward, basic differentiation medium was used for organoid culture.

extract_protocol:
Total RNA was isolated from cells using Trizol (Invitrogen). RNA was purified using Quick-RNA kit (Zymo Research) with DNase treatment.
RNA samples of high integrity were used for RNA-seq library construction. rRNA depletion was conducted followed by library construction with NEBNext Ultra RNA Library Prep Kit. Constructed libraries were multiplexed and 150 bp paired-end sequenced with Illumina HiSeq 4000.

treatment_protocol: To generate 3D kidney organoids, day 10-12 differentiating cells were dissociated into single cells by Accutase. 2.5-5 x 104 cells (per well) were aggregated in basic differentiation media supplemented with 50 ng/mL FGF9 and 10 μM Y-27632 using round bottom ultra-low attachment 96-well plates (Corning). 24 hours later, Y-27632 was removed. To generate kidney organoids with a high glomerulus-to-tubule ratio, no patterning CHIR was needed. To generate kidney organoids with a high tubule-to-glomerulus ratio, 10 days patterning CHIR was applied from day 14 to day 24 of differentiation. 3D kidney organoids were transferred onto the upper chamber of transwell (Corning) for liquid-air interface culture on day 16-18 of differentiation (5-7 days after aggregation), with daily medium change at the bottom chamber. Taking H9 ESCs as an example, we seeded ~21,000 cells per cm2, and started differentiation when the cells reached 50-60% confluence. On day 10-12 of differentiation, we dissociated the differentiation culture into single cells, and re-aggregated into cell clusters with a gradient of cell numbers (5,000-75,000 cells per organoid). One million starting human ESCs could give rise to approximately 3,500 kidney organoids that were aggregated with 35,000 cells per organoid. hPSC-derived 3D kidney organoids were implanted beneath the renal capsule of left kidney of NSG mice for easier manipulation. After 2-4 weeks mice were sacrificed, and implants were isolated for further analysis.

value: Human pluripotent stem cells

value: Kidney organoid

tag: developmental stage

value: in vivo 4 weeks


title: kidney organoid, invivo_4weeks_3

status: Public on May 29 2019

type: SRA

city: London

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue


title: RH41 LAQ824 low

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

description: Paired-end

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR.
Gene expression values were calculated as Transcripts per Million (TPM) using STAR and the UCSC reference at the gene level.
Differential gene expression was determined using EdgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM files are provided in txt format at the gene-level.

source_name: FP-RMS cell line, PAX3-FOXO1

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
RNA was extracted from FP-RMS cell lines using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: Drug was dissolved in DMSO to a stock concentration of 10 mM, and additionally diluted in DMEM to a final concentration of 0.5, 1, 5, or 10 µM (or DMSO of equivalent final volume), exposing cells for 1, 6 or 24 hours before extracting RNA.

tag: cell line

value: FP-RMS cell line

tag: treatment time

value: 6 hours

tag: treatment

tag: drug target

value: HDAC


title: kidney organoid, invivo_2weeks_3

value: in vivo 2 weeks


title: kidney organoid, invivo_4weeks_1


title: RH41 LAQ824 high

description: Paired-end

value: LAQ824 5 uM


title: 129

type: RNA

city: Adelaide

first: Chung

middle: H

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

description:
CP-CML
sample_61

hyb_protocol: A total of 12 different labelled samples can be loaded into 12 individual arrays per beadchip.  The chip was then hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.  Upon completion of the washing, the chips were then coupled with Cy3.

scan_protocol: scanned in the Illumina iScan Reader. The scanner operating software, GenomeStudio version 1.9.0, converts the signal on the array into a TXT file for analysis.

data_processing: Normalisation was performed using neqc function implemented in limma (Bioconductor) package.

label: biotin

label_protocol: A total of 500ng of total RNA was then prepared for hybridisation to the Ilumina humanHT 12 Expression Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip). A total hybridisation volume of 15ul was prepared for each sample and 15ul loaded into a single array on the Ilumina humanHT 12 Expression Beadchip.

extract_protocol: RNA was extracted with Trizol reagent, followed by  QIAGEN miRNeasy midi kit in accordance with the prescribed protocol provided with the kit. The quality and quantity of human total RNA was ascertained on the Agilent Bioanalyser 2100 using the NanoChip protocol.

tag: gender

value: Male

tag: age

tag: disease stage

value: diagnostic chronic phase

tag: bcr-abl1 at 3 month


title: RH41 JQ1 low

description: Paired-end

value: JQ1 0.5 uM


title: 133

description:
CP-CML
sample_63


title: RH41 JQ1 high

description: Paired-end

value: JQ1 5 uM


title: kidney organoid, invivo_2weeks_1


title: RH41 GSKLSD1 low

description: Paired-end

value: GSKLSD1 1 uM

value: Lysine Specific Demethylase 1 (LSD1)


title: kidney organoid, invivo_2weeks_2


title: 134

description:
CP-CML
sample_60


title: kidney organoid, Day24_2


title: 125

description:
CP-CML
sample_59


title: 121

description:
CP-CML
sample_57

value: Female


title: 120

description:
CP-CML
sample_55


title: 122

description:
CP-CML
sample_56


title: kidney organoid, Day10_2


title: 117

description:
CP-CML
sample_52


title: 130

description:
CP-CML
sample_58


title: 100

description:
CP-CML
sample_49


title: 118

description:
CP-CML
sample_54


title: RH41 GSKLSD1 high

description: Paired-end

value: GSKLSD1 10 uM


title: RH41 GSKJ4 low

description: Paired-end

value: GSKJ4 0.5 uM


title: kidney organoid, Day10_1

value: Human pluripotent stem cells


title: kidney organoid, Day24_1

value: Kidney organoid


title: 105

description:
CP-CML
sample_51


title: kidney organoid, Day0_2


title: 92

description:
CP-CML
sample_47


title: RH41 GSKJ4 high

description: Paired-end

value: GSKJ4 5 uM


title: RH41 EZ-005 low

description: Paired-end

value: FP-RMS cell line


title: 80

description:
CP-CML
sample_44


title: 75

description:
CP-CML
sample_39


title: 74

description:
CP-CML
sample_41


title: kidney organoid, Day0_1


title: RH41 EZ-005 high

description: Paired-end

value: 6 hours


title: WGBS_KO

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: Whole genome bisulfite-treated DNA

library_source: genomic

data_processing:
WGBS: The raw 2x150bp reads were trimmed for adapter sequences and low quality reads with trimmomatic (Bolger et al., 2014) using a sliding window of 4 bases, with quality cut-off at 20. The 20 leading and trailing bases were trimmed if below 20. Reads with less than 50 bases after trimming were discarded. Furthermore, the first 20 bases on read mate 2 were cropped using cutadapt due to overrepresentation of guanine bases. Fastqc was used to assess quality.    The trimmed and filtered reads were further processed with Bismark (Krueger and Andrews, 2011). Bisulfite genome conversion and indexing was done with bowtie2 (Langmead and Salzberg, 2012) running bismark_genome_preparation, before running Bismark mapping, deduplication and methylation extraction, using --no_overlap to avoid coverage bias.
Genome_build: hg38
Supplementary_files_format_and_content: Coverage file: (Chr - Start - End - #reads supporting methylated C - #reads supporting unmethylated C)

molecule: genomic DNA

source_name: fetal-derived neural progenitor cells (sai)

growth_protocol: The DNMT1-KO and subsequent analysis was performed on the embryo-derived human neural epithelial-like stem cell line, Sai2 (Tailor et al., 2013), and was maintained as previously described (Falk et al., 2012).

extract_protocol: The Accel-NGS Methyl-Seq DNA Library

treatment_protocol: LV.gRNA.CAS9GFP vectors (Liao et al., 2015) were used to target DNMT1 (DNMT1-KO) or LacZ (control). Lentiviral vectors were produced as previously described (Zufferey et al., 1997) and were of titers 109 TU/ml which was determined using qRT-PCR (Georgievska et al., 2004). hNPCs were transduced with an MOI 10-15 and allowed to expand 10 days prior to FACS (FACSAria, BD sciences). Cells were detached and resuspended in basic culture media with Rock inhibitor (10µM, Miltenyi) and propidium iodide (BD Bioscience), and strained (70µm, BD Bioscience). GFP positive cells were spun down (400g, 7min) and snap frozen on dry ice. Cell pellets were kept at -80°C until RNA was isolated. All groups were performed in biological triplicates

tag: viral vector

tag: grna target

value: DNMT1 exon 32


title: RH41 DMSO low rep2

description: Paired-end

value: DMSO 0.1%

value: control


title: RH41 DMSO low rep1

description: Paired-end


title: 87

description:
CP-CML
sample_45

value: Male


title: 81

description:
CP-CML
sample_43

value: diagnostic chronic phase


title: WGBS_CTR

description: Whole genome bisulfite-treated DNA

value: fetal-derived neural progenitor cells (sai)

value: LacZ


title: RH41 DMSO high rep2

description: Paired-end

value: DMSO 0.2%


title: RH41 DMSO high rep1

description: Paired-end


title: VCK2

city: Beijing

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

country: China

institute: University of Chinese Academy of Sciences

data_processing:
The reads were trimmed using FASTX-Toolkit (version 0.11.5)
The clean reads were mapped to the grape genome by using tophat (version 2.0.14) with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks (version 2.2.1).
Genome_build: 12X grape genome of IGGP
Supplementary_files_format_and_content: tab-delimited text file include FPKM values of all samples.

organism: Vitis amurensis

source_name: control

growth_protocol: Vitis amurensis plantlets were grown on 1/2 MS (pH 5.8, 30 g l.1 sucrose, 0.7% agar) at 26 °C and 16 h light photoperiod

extract_protocol:
We isolated total RNA from three controls and three grape transgenic calli lines (100mg per sample), using RNAprep pure plant kit (Qiagen, China) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The whole coding sequence of VvSWEET10 was from Vitis vinerfera chardonnay and cloned into a binary vector pSAK277, the resulting plasmids were transformed into V. amurensis petiole according to the method of Zhao et al., 2017 (doi: 10.1371/journal.pone.0179730<https://dx.doi.org/10.1371%2Fjournal.pone.0179730>).

value: callus

tag: genotype

value: wildtype


title: 90

description:
CP-CML
sample_46

value: Female


title: 180

description:
CP-CML
sample_94


title: VCK1


title: RH41 Cpd50 low

description: Paired-end

value: Cpd50 0.5 uM

value: Pan Jumonji


title: 150

description:
CP-CML
sample_74


title: VCK3


title: V103

source_name: VvSWEET10 gene transgenic

value: expresses Vitis vinifera chardonnay VvSWEET10 gene


title: RH41 Cpd50 high

description: Paired-end

value: Cpd50 5 uM


title: 70

description:
CP-CML
sample_38


title: 71

description:
CP-CML
sample_37


title: V102


title: 58

description:
CP-CML
sample_34


title: RH41 Bromosporin low

description: Paired-end

value: FP-RMS cell line

value: Bromosporin 1 uM

value: Bromodomains


title: 63

description:
CP-CML
sample_33


title: 56

description:
CP-CML
sample_31


title: V101


title: 52

description:
CP-CML
sample_29


title: 46

description:
CP-CML
sample_26


title: 48

description:
CP-CML
sample_27


title: 55

description:
CP-CML
sample_30


title: 47

description:
CP-CML
sample_23


title: 49

description:
CP-CML
sample_25


title: 43

description:
CP-CML
sample_21


title: RH41 Bromosporin high

description: Paired-end

value: 6 hours

value: Bromosporin 10 uM


title: 39

description:
CP-CML
sample_19

value: Male


title: 42

description:
CP-CML
sample_22

value: diagnostic chronic phase


title: RH4 PLX2

description: Paired-end

value: PLX2 1 uM


title: 41

description:
CP-CML
sample_20


title: Apical B-- Library2

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

country: Spain

institute: CABD

data_processing:
Each sample was mapped against the index genome built from oryLat2 assembly using Hisat2 (Kim et al., 2015)
The aligned read SAM files were assembled into transcripts, their abundance was estimated and tested for differential expression by Cufflinks  v2.2.1(Trapnell et al., 2012)
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Cufflinks output) and DEGs analysis (Cuffdiff output)

organism: Oryzias latipes

source_name: Gill filaments

extract_protocol:
Manual dissection of apical and central domain of gill. Trizol was used to extract Total RNA.
poly A selection for the RNA from the NEBnext Poly A module

value: Adult

tag: strain

value: Cab

value: Gill - Branchial Arch


title: 45

description:
CP-CML
sample_24


title: 38

description:
CP-CML
sample_18


title: 23

description:
CP-CML
sample_17


title: 21

description:
CP-CML
sample_11


title: 30

description:
CP-CML
sample_14


title: RH4 PLX1

description: Paired-end

value: PLX1 1 uM


title: 17

description:
CP-CML
sample_16

value: Female


title: Apical B- Library1


title: 18

description:
CP-CML
sample_7


title: RH4 N1302

description: Paired-end

value: HDAC


title: 11

description:
CP-CML
sample_6


title: 19

description:
CP-CML
sample_9


title: GR84

city: Boulder

first: Christopher

last: Link

state: Colorado

address: 1725 Pleasant st

department: Integrative Physiology

institute: University of Colorado Boulder

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina Adaptors were removed and low quality regions (phred minimum of 20) were trimmed using a sliding window with Trimmomatic (v 0.36). Trimmed reads with lengths less than 36 bases were removed.
To generate gene counts we aligned all trimmed and filtered fastq files to mm10 using STAR v2.5.2b using default paramaters with --quantMode GeneCounts enabled.
To generate repetitive element counts we used the Repenrich2 algorithm with the mm9 genome.
Genome_build: mm9 for repetitive elements analysis, mm10 for gene expression analysis
Supplementary_files_format_and_content: Gene counts are tab-delimited text files consisting of a geneID column, unique aligned counts for unstranded RNA-seq, 1st read strand aligned, and 2nd read strand aligned.
Supplementary_files_format_and_content: Repetitive element counts are tab-delimited text files with columns consisting of  repetitive elements, their repetitive element class, repetitive element family, and count.

molecule: polyA RNA

organism: Mus musculus

source_name: hippocampus and cortex homogenate

extract_protocol:
To extract total RNA in mouse brain, 1 volume of brain homogenate was mixed with 3 volumes of Trizol LS Reagent (10296010, Thermo Fisher Scientific), and frozen on dry ice. One day later, total RNA was extracted using the Direct-zolTM RNA MiniPrep kit (R2073, Zymo Research) according to the manufacturer’s instruction.
A total of 200 ng of RNA in a 50 μl volume was used for preparation of paired-end sequencing libraries using the TruSeq Stranded Total Sample Preparation kit (Illumina).

treatment_protocol: Intracerebroventricular (ICV) injections of virus in post-natal day 0 (P0) C57BL/6J pups was  performed  using 2  μl  (1×1010  genomes/μl)  of  AAV1-GFP, AAV1-GFP-(PR)50, or AAV1-GFP-(GR)100 solution per cerebral ventricle.

value: 3 months

tag: aav vector

tag: Sex

value: M

tag: grouping


title: GR145

value: F


title: Central A-- Library2

tag: developmental stage


title: Central B

tag: tissue


title: GR140


title: GR114


title: RH4 DMSO

description: Paired-end

tag: cell line

tag: cell type

value: FP-RMS cell line

value: DMSO 0.1%

value: control


title: GR82

value: AAV-GFP

value: GR-control


title: 16

description:
CP-CML
sample_5


title: 2

description:
CP-CML
sample_2

value: Male


title: Apical A


title: 22

description:
CP-CML
sample_8

value: diagnostic chronic phase


title: GR119


title: GR118


title: PR24


title: PR25


title: 3

description:
CP-CML
sample_1


title: 4

description:
CP-CML
sample_3


title: IPF2

city: Bad Nauheim

first: Karla

last: Rubio

address: Parkstrasse 1

department: Lung Cancer Epigenetics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Visualization of raw reads was done using FastQC, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), using the following parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40 CROP:45 HEADCROP:5
High quality reads were aligned to the hg19 genome by using bowtie2 (-D 15 -R 3 -N 0 -L 20 -i S, 1, 0.56 -p8),
Sam files were converted to bam files using samtools view and sort.
The tag libraries were created by using MakeTaglibrary from HOMER 29, (-format sam) for the samples mapped to NONCODE, The sorted bam files were further converted to fastq files with SamToFastq.jar from  picard-tools-1.119 (https://sourceforge.net/projects/picard/files/picard-tools/1.119/) to convert the bam to fastq files and remapped to hg19 (UCSC reference genome) in order to make the bedgraph files
analyzeRepeats.pl (http://homer.salk.edu/homer/ngs/analyzeRNA.html) with the parameters (analyzeRepeats.pl  database.gtf hg19 -count genes -strand both and -rpkm; reads per kilobase per millions mapped). The NONCODE_V.4.gtf file was used to quantify ncRNA
makeUCSCfile (default) from homer were used to obtained the Bedgraph file to load in the UCSC genome Browser
Genome_build: Human hg19  and NONCODE V4.0
Supplementary_files_format_and_content: text file with FPKM data, bedgraph

source_name: Primary fibroblasts_nuclear_RNA

growth_protocol: Primary fibroblast from Ctrl and IPF patients were cultured in complete MCDB131 medium (8% FCS, 1% L‐glutamine, penicillin 100 U/ml, streptomycin 0.1 mg/ml, EGF 0.5 ng/ml, bFGF 2 ng/ml, and insulin 5 μg/ml)) at 370C in 5% CO2.

extract_protocol:
Ctrl and IPF primary fibroblasts nuclei from 2 different patients each were isolated after treatment with hypotonic solution (50 mM Tris-HCl pH 6.5, 2 mM EGTA, 0.1% NP40, 10% Glycerol, 0.2 mM DTT, 20 mM NaF, 20 mM Na3VO4, 40   g/ml phenylmethylsulfonyl fluoride, protease inhibitor and RNase inhibitor in DEPC treated water) and used for nuclear total RNA isolation with Trizol (Invitrogen) and quantified using a Nanodrop Spectrophotometer (ThermoFisher Scientific, Germany).
RNA sequencing (RNA-seq) of nuclear extracts from Ctrl and IPF primary fibroblasts was performed by Single End (SE) sequencing using Nextseq500 (Illumina) sequencer with V2 chemistry. RiboGone™ - Mammalian (Clontech) was used to deplete ribosomal RNA from the samples. SMARTer® Universal Low Input RNA Kit for Sequencing (Clontech) was used for pre-amplification before library preparation. Library preparation was performed using the Low Input Libray Prep Kit (Clontech) following the manufacturer’s instructions.

value: Fibroblasts

tag: diagnosis

value: IPF

tag: passages

value: Passage 3

value: male


title: PR19


title: PR18


title: PR17


title: IPF 1

tag: gender


title: GR80

tag: age


title: PR15


title: Central A - Library1

value: Adult

value: Cab

value: Gill - Branchial Arch


title: PR23

value: 3 months

value: PR-control


title: PR12

value: M


title: Donor 2

value: healthy


title: Donor 1


title: PR20

value: F


title: WT pollen RNA-seq rep7

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

description:
mikado-permissive.superloci.gff
TAIR10_gene_plus_mikado_TE_transcripts.gff
This sample was used only for TE transcript identification and not the RPKM calculations.

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-Seq: TE transcript annotation was created using four biological replicates of pollen RNA-seq data. Tophat2, Hisat, and STAR were used to align the RNA-seq reads to the TAIR10 genome
Transcripts were assembled using CLASS2, StringTie, and Cufflinks, respectively.
Assembled transcripts were selected by Mikado using default options except the BLAST and Transdecoder steps were disabled. As a result, 21381 transcripts (called superloci) were identified and included in the output file called mikado-permissive.superloci.gff.
The list of superloci was refined by selecting those overlapping with TAIR10 TE annotation.
TE-like genes were eliminated from the refined list if their CG methylation is less than 0.7 in rosette leaves. This gave rise to an annotation of TE transcripts.
The annotation of TE transcripts was combined with TAIR10 gene annotation for Kallisto analysis which gives rise to the output files named abundance.tsv.
Genome_build: TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

organism: Arabidopsis thaliana

source_name: WT pollen

growth_protocol: plants were grown in LD condition (16h lights/8h darkness) at 22-24 degrees

extract_protocol:
follow the instruction of Mirvana miRNA isolation kit
follow the instructions of Ovation RNA-Seq Systems 1–16 for Model  Organisms kit

value: whole pollen

value: WT


title: PR16

value: AAV-GFP


title: T24_siG9a_rep1

city: Shanghai

first: Jingya

last: Sun

address: 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

hyb_protocol: Following Fragment and Label Single-Stranded cDNA, 27ul of biotin-labeled ss-cDNA sample were hybridized for 16 hr at 45℃ on GeneChip Clariom S Human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with robust multi-array average (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChipTM WT PLUS Reagent Kit, 2017, Affymetrix)

growth_protocol: T24 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum.

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

treatment_protocol: T24 cells were seeded in 6-well plates at 30% conference. After 24 h, cells were transfected with negative control siRNA or G9a siRNA using Lipofectamine RNAiMAX. Then, the cells were cultured for another 48 h and then prepared using Trizol.

value: bladder cancer cells

tag: treatment

value: G9a siRNA


title: hHB11w

data_processing:
Alignment: For all RNAseq data sets, the sequencing reads were mapped to the human reference genome (hg38) using STAR aligner v2.5.0a (Dobin et al., 2013)
Align for coding gene analysis: For quantification of NCBI genes (O'Leary et al., 2016) entries, reads mapping to 10 or less positions were kept and the primary alignments were used for quantification. Mapping was performed with splice junction overhang of minimum one base, assisted by Gencode v25 annotation.
Align for retroelement analysis: The analysis of retrotransposons only included uniquely mapped reads (-- outFilterMultimapNmax 1). A maximum of 0.03 mismatches per base were allowed (--outFilterMismatchNoverLmax 0.03).
Genes and TEs were quantified using the Subread package FeatureCounts (Liao et al., 2014).
RepeatMasker annotation for hg38 was downloaded from the UCSC table browser (Karolchik et al., 2004).
Genome_build: hg38
Supplementary_files_format_and_content:
hEmbryo_PE150.hg38.mMap.NCBI.sense.txt: Count table of NCBI genes. First line: Run info in featureCounts. Second line: Header describing content of each column. From third line starts count data for each given gene
hEmbryo_PE150.hg38.unique.ERE.notInExon.NCBI.NONstrandSpecific.txt: Count table of RepeatMasker retroelements, quantified without specifying sense/antisense mapping. First line: Run info in featureCounts. Second line: Header describing content of each column. From third line starts count data for each given gene
hEmbryo_PE150.hg38.unique.ERE.notInExon.NCBI.ANTISENSE.Srf.txt: Count table of RepeatMasker retroelements, quantified only fragments mapping in antisense direction to the element. First line: Run info in featureCounts. Second line: Header describing content of each column. From third line starts count data for each given gene
hEmbryo_PE150.hg38.unique.ERE.notInExon.NCBI.sense.txt: Count table of RepeatMasker retroelements, quantified only fragments mapping in sense direction to the element. First line: Run info in featureCounts. Second line: Header describing content of each column. From third line starts count data for each given gene

source_name: human fetus

extract_protocol:
miRNeasy Micro Kit (Qiagen) KAPA stranded RNA-seq with RiboErase kit.
Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq500 (PE 2x150bp)

tag: fetal region

value: hindbrain

value: fetal-derived neural progenitor cells


title: T24_siG9a_rep2


title: PR11


title: T24_siG9a_rep3


title: hCtx9w

value: cortex


title: T24_siNC_rep2

source_name: T24_siNC_48 h

value: negative control siRNA


title: T24_siNC_rep1


title: hDienc9w

value: diencephalon


title: hVM6_5w

value: 6w 5d

value: ventral midbrain


title: hVM11w


title: hSC11w

value: spinal cord


title: Male gonad_rep3

city: Guangzhou

first: Linmiao

last: Li

address: Xin-Gang-Xi-Lu 105

institute: Guangdong Institute of Applied Biological Resources

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression). For two experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the ANOVA Method (O'Mahony, Michael (1986) were calculated; Log2 (median treat(F1a,F2a,F3a)/median control (M1,M2,M3)signal) ratios; median are derived from LOWESS normalized data from all probes per sRNA.
limma package;R language(Parameter 1: normalized:quantile; Parameter 2:pvalue-method:T-test; Parameter 3:foldchage:2 times)

organism: Acipenser schrenckii

source_name: Male gonad

label_protocol: The assay started from 2 ug total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; Cy5 was used for the each RNA sample in experiments.

extract_protocol: Total RNA was extracted using miRNeasy Kit(Qiagen, 217004), following the manufacturer's recommended protocol.

value: male

value: gonad


title: Male gonad_rep1


title: T24_siNC_rep3


title: Male gonad_rep2


title: MCF10A_Satb1_TMP_seq

status: Public on May 28 2019

city: Stanford

first: Jan

last: Liphardt

state: California

address: 443 Via Ortega, Shriram Center 020

department: Bioengineering

institute: Stanford university

data_processing:
Library strategy: TMP-seq
reads are filtered and trimed with Cutadapt
reads are aligned to genome using Bowtie2
MACS2 is used for peak calling for CHIP-seq and ATAC-seq
Differential binding in CHIP-seq was performed with DESeq2 package in r.
Genome_build: hg19; mm10

source_name: human mammary gland epithelial cell line

growth_protocol: MCF10A expressing satb1 fusion are maintained in DMEM/F12 with supplements as described. Vl3 cells are maintained in RPMI supplemented with 10% FBS

extract_protocol:
In CHIP-seq, cells are fixed, washed, and lysed to purify the nuceli. Then chromatin were fragmented with Covaris, and mixed with antibody and beads to pull down the bound fraction as described in the manuscript. In TMP-seq, protein and RNA are first crosslinked in TMP solution with UV; then genomic DNA are purified and sheared with Covaris. In ATAC_seq, the 50,000 cells are washed and tagmented by Tn5 for 30min.
Standard CHIP-seq libraries made using NEBnext Ultra II kit from chipped DNA. TMP_seq and ATAC-seq libraries were constructed following published protocols.
CHIP-seq and TMP_seq were sequencing in Illuma in Single end. ATAC_seq were sequenced in Paired end.

treatment_protocol: when applicable, the cells are treated camptothecin or ICRF-193 for 2hr before being fixed to prepare CHIP-seq libraries

value: epithelial

tag: antibody


title: MCF10A_ICRF_TMP_seq


title: MCF10A_Satb1_ICRF_TMP_seq


title: Female gonad_rep3

source_name: Female gonad

value: female


title: MCF10A_Satb1_CP_TMP_seq


title: MCF10A_genomicDNA_TMP_seq


title: MCF10A_ATAC_seq

data_processing:
reads are filtered and trimed with Cutadapt
reads are aligned to genome using Bowtie2
MACS2 is used for peak calling for CHIP-seq and ATAC-seq
Differential binding in CHIP-seq was performed with DESeq2 package in r.
Genome_build: hg19; mm10


title: Root of control (untreated) Brassica napus, biological replicate 3

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were quantified with Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Brassica napus

source_name: Root of Brassica napus, left untreated for 4 days

label_protocol: Biotinylated cRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Seeds of oilseed rape (Brassica napus L. cv. Nourin No.16, Kaneko Seed Co. Ltd., Gumma, Japan) were germinated in vermiculite by using bottom irrigation. Modified Hoagland solution (nutrient solution), described previously [Soil Sci. Plant Nutr. 54 (2008) 118–127.], was used as the irrigation solution. At 10 days after germination, young seedlings were transferred to 1.5-L containers (4 seedlings/container) containing 1.2 L of the nutrient solution, and the containers were maintained in a growth chamber for a 16-h photoperiod (~200μmol m-2s-1) at 24 °C, and at 16°C at night. Nutrient solutions were aerated continuously and renewed twice weekly. Each tested plant was grown for 4 weeks before being harvested.

extract_protocol: Total RNA was isolated using an RNeasy Plant kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Plants were exposed to glutathione for 4 days. GSH (glutathione, reduced form) was applied to source leaves (fully expanded leaves). In the leaf GSH treatment, 50 µL of 100 mM GSH in a foliar-application solution (10 mM MES-KOH, pH6.1, 0.01% [w/v] Triton X-100) was applied to each leaf with a painting brush; GSH was applied to 3 expanded leaves per plant daily before harvest.

value: Nourin No.16

tag: agent

value: root

tag: growth stage

value: 4 weeks after germination


title: MCF10A_Satb1_ATAC_seq


title: Female gonad_rep1


title: Root of foliar GSH-treated Brassica napus, biological replicate 2

description: No additional information

source_name: Root of Brassica napus, after 4 days of foliar GSH treatment

tag: strain

value: GSH (glutathione, reduced form)


title: Root of foliar GSH-treated Brassica napus, biological replicate 3

description: No additional information


title: 10 mM acetic acid-treated leaves, biological rep3

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

description: Gene expression data

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi.

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified.

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Manihot esculenta

source_name: 10 mM acetic acid-treated leaves

label_protocol: The five hundred ng of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 6.0 mM of Cy3-CTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

growth_protocol: After reaching an approximate stem length of approximately 15 cm from soil surface, the plants were transferred to a plastic pot (7.9 diameter x 6 height cm) with vermiculite. After transfer, they were incubated at 28 degree in a greenhouse for 2 weeks.

extract_protocol: Total RNA from leaves was purified according to manual protocol using RNeasy Plant Mini kit protocol (QIAGEN) followed by Plant RNA reagent protocol (Invitrogen). The total RNA quality was evaluated by electrophoresis with the bioanalyzer system (Agilent, USA). The total RNA was stored at -80ºC until further use.

treatment_protocol: The plants of approximately 20 cm stem were treated with 10 mM acetic acid or water (control) for 7 days, and exposed to drought treatments for 14 days.

value: plants of approximately 20 cm stem

tag: pre-treatment

value: 10 mM acetic acid for 7 days

value: drought for 14 days

tag: tag

value: the first to third leaves


title: Root of foliar GSH-treated Brassica napus, biological replicate 1

description: No additional information


title: Water-treated leaves, biological rep2

description: Gene expression data

source_name: Water-treated leaves

value: water (control) for 7 days


title: MCF10A_CP_TMP_seq


title: MCF10A_Satb1_ICRF_CHIP_seq

value: GFP antibody


title: 10 mM acetic acid-treated leaves, biological rep1

description: Gene expression data


title: Root of control (untreated) Brassica napus, biological replicate 1

description: No additional information


title: Water-treated leaves, biological rep3

description: Gene expression data


title: Root of control (untreated) Brassica napus, biological replicate 2

description: No additional information


title: MCF10A_Satb1_CP_CHIP_seq


title: Female gonad_rep2

tag: Sex


title: 10 mM acetic acid-treated leaves, biological rep2

description: Gene expression data


title: VPA day21 Rep3

city: STANFORD

first: Cheen Euong

last: Ang

state: CA

address: 265 Campus Drive

institute: Stanford

data_processing:
Sequences were mapped with Tophat to hg19. RPKM is calculated using Cuffdiff.
FPKM values reported by cuffdiff are combined into an excel spreadsheet file.
Genome_build: hg19
Supplementary_files_format_and_content: txt file containing the read counts values for all the samples.

source_name: hES-iN_VPA day28

growth_protocol: Human neurons were generated by directed reprogramming of embryonic stem cells using overexpression of Neurogenin-2. Cells were cultured in N3 and Neurobasal media, according to Zhang et al., Neuron, 2013.

extract_protocol:
Cells were dissociated, and isolated using fluorescence activated cell sorting. Cells were then resuspended directly in TRIzol reagent, and the RNA was extracted according to manufacturer's protocol.
The libraries were constructed using the Ultra Low Input RNA kit, or the TruSeq kit.

treatment_protocol: The reprogrammed human neurons were treated with Valproic acid at day 1, day 21, or day 50-56, and analyzed after 72-96 hr.

value: hES derived induced neurons (hES-iN)

value: Valproic acid


title: VPA day21 Rep4


title: VPA day21 Rep2


title: VPA day21 Rep1


title: VL3_NC1_CHIP_seq

source_name: mouse T cells

value: lymphocyte


title: Ctrl day21 Rep3

source_name: hES-iN_Ctrl day28

value: control


title: Ctrl day21 Rep4


title: VL3_dHD_CHIP_seq


title: Ctrl day21 Rep1


title: MCF10A_TMP_seq


title: VL3_Satb1_CHIP_seq

value: Satb1 antibody


title: WT_OL_Day14_Rep3

city: New York

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

data_processing:
Quality assessment and fold change calculations were performed in edgeR
Sequencing data was quality checked using FastQC, aligned to the reference genome (mm10, UCSC, Santa Cruz, CA, USA) with the STAR software package
Differential expression based on counts per million mapped reads was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: edgeR

source_name: WT_OL_Day14_plantaris tendon

extract_protocol:
RNA was purified with a miRNeasy Micro Kit (Qiagen) supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher). For each sample, 250ng of RNA was delivered to the University of Michigan Sequencing Core for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: ScxCreERT2-/- IGF1Rflox/flox

tag: tamoxifen treatment

value: Yes

value: Plantaris tendon


title: KO_OL_Day14_Rep1

source_name: KO_OL_Day14_plantaris tendon

value: ScxCreERT2+/+ IGF1Rflox/flox

tag: tissue


title: KO_OL_Day7_Rep3

source_name: KO_OL_Day7_plantaris tendon


title: KO_OL_Day14_Rep4


title: WT_OL_Day14_Rep2


title: KO_OL_Day14_Rep3


title: WT_OL_Day14_Rep1


title: KO_OL_Day14_Rep2


title: KO_OL_Day7_Rep4


title: KO_OL_Day7_Rep1


title: VL3_CHIP_input

tag: cell type

tag: cell line


title: WT_OL_Day7_Rep4

source_name: WT_OL_Day7_plantaris tendon


title: Ctrl day21 Rep2


title: WT_OL_Day7_Rep3


title: KO_OL_Day7_Rep2


title: WT_NOC_Day0_Rep2

source_name: WT_NOC_Day0_plantaris tendon

value: No


title: WT_NOC_Day0_Rep4


title: WT_OL_Day7_Rep1


title: Water-treated leaves, biological rep1

description: Gene expression data


title: WT_NOC_Day0_Rep3


title: WT_NOC_Day0_Rep1


title: WT_OL_Day7_Rep2


title: WT_OL_Day14_Rep4


title: IGF1_24h_Rep1

source_name: IGF1_24h_tail tendon

extract_protocol:
RNA was purified with a miRNeasy Micro Kit (Qiagen) supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher). For each sample, 500ng of RNA was delivered to the University of Michigan Sequencing Core for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

tag: cytokine treatment

value: IGF1 (100ng/mL)

tag: igf1 treatment time

value: 24 hours

value: Tail tendon


title: IGF1_24h_Rep4

tag: age


title: IGF1_6h_Rep4

source_name: IGF1_6h_tail tendon

value: 6 hours


title: IGF1_24h_Rep3


title: H10 rep1

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: Affymetrix GeneChip Hybridization Wash and Stain Kit (PN:  900720) protocol was used for all hybridization, wash and staining steps.  Fragmented and labeled cDNA (130 μL at 25 ng/μL) were hybridized for 17 hr at 45° C to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays (PN: 902119).

scan_protocol: Chips were washed and stained on an Affymetrix Genechip Wash Station 450 using the FS450_0002 protocol and scanned on the Affymetrix GeneChip Scanner 3000. *.cel files were generated for analysis using Affymetrix GeneChip Command Console v3.2.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (GeneChip™ Mouse Gene 2.0 ST Array), and array data were analyzed using Transcriptome Analysis Console 4.0 software (ThermoFisher Scientific).

label: Ambion WT Expression Kit (4411974) and Affymetrix GeneChip WT Terminal Labeling Kit (900671)

source_name: CD4+CD25+ Treg

label_protocol: Sense-strand single-stranded cDNA was prepared from 200 ng of total RNA using the Ambion WT Expression Kit (PN:  4411974).  Both cRNA and cDNA were assessed using UV absorbance.  5.5 μg of single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN: 900671).

growth_protocol: Female HDAC10–/– and wild type control mice (C57BL/6, (8-12 weeks old) mice were housed in the CHOP animal facility.

extract_protocol: RNA was isolated using RNeasy kits (QIAGEN). Total RNA was assessed by UV absorbance and all had 260/280 nm ratios above 1.7.  Additionally, samples were run on the Agilent RNA 6000 Nano chip and all had RINs in the 8.0 range.

treatment_protocol: CD4+CD25+ regulatory T cells (Treg) were isolated (n=3 indepndent samples per group)

tag: genotype


title: IGF1_6h_Rep3


title: IGF1_2h_Rep4

source_name: IGF1_2h_tail tendon

value: 2 hours


title: IGF1_1h_Rep4

source_name: IGF1_1h_tail tendon

value: 1 hour


title: IGF1_2h_Rep2


title: IGF1_1h_Rep3


title: IGF1_2h_Rep1


title: H10 rep3


title: WT rep1


title: WT rep3


title: IGF1_6h_Rep2


title: IGF1_6h_Rep1


title: H10 rep2


title: WT rep2


title: IGF1_2h_Rep3


title: IGF1_1h_Rep2


title: IGF1_1h_Rep1


title: IGF1_0h_Rep3

source_name: IGF1_0h_tail tendon

value: 0 hours


title: IGF1_0h_Rep2


title: vitro_Foxo3dNES_Tg_D21_Hypoxia_rep2

city: Fukuoka

first: So

last: Shimamoto

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku

department: Department of Developmental Stem Cell Biology

institute: Kyushu-university

data_processing:
RNA-seq reads were processed with the FASTX tool kit (v0.0.14, Patel and Jain, 2012) to remove short (<20 bp) and low quality (quality score <20) reads, followed by trimming of the adaptor sequence.
Processed reads were mapped to the mouse mm10 genome using TopHat2/Bowtie2 (v2.0.13, Kim et al., 2013).
Mapped reads were counted by featureCounts(v1.5.1, Liao et al., 2014)
RPM values were calculated using R software(v.3.4.4)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including RPM values for each sample.

source_name: In vitro D21 Foxo3dNES Tg oocyte cultured under hypoxia

growth_protocol: In vivo oocytes were isolated from stella-ECFP(SC) reporter transgenic ovaries at various developmental stages.  In vitro oocytes induced from mouse ESCs were isolated from reconstituted ovaries (rOvaries) at various date of culture as described previously (Hikabe et al., 2016) To produce one rOvary, 5000 Blimp1-mVenus (BV)-positive PGCLCs and 75,000 frozen-thawed E12.5 gonadal somatic cells were aggregated and cultured on Transwell-COL membranes (IVDi culture). WT ESCs and Foxo3dNES Tg ESCs were subjected to IVDi culture for 21 days under the normoxic (5% CO2 and air) or hypoxic condition (5% O2, 7% CO2 and 93%N2) to obtain in vitro D21 oocytes. 10 μM of Rock inhibitor (Y-27632) was added for the first 2 days in the IVDi culture.

extract_protocol:
A directional RNA-seq library was prepared as described previously (Hamazaki et al. 2015). Briefly, poly(A)+ RNAs were extracted from the oocytes by using a Dynabeads mRNA DIRECT Micro Kit (Invitrogen).
cDNA libraries were constructed from purified poly(A) RNA using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). cDNA libraries were amplified by 12-cycle PCR and checked for length distribution.

value: oocyte


title: vitro_Foxo3dNES_Tg_D21_Hypoxia_rep1


title: vitro_WT_D21_Hypoxia_rep1

source_name: In vitro D21 WT oocyte cultured under hypoxia


title: vitro_WT_D21_Hypoxia_rep2


title: IGF1_24h_Rep2


title: vitro_Foxo3dNES_Tg_D21_Normoxia_rep2

source_name: In vitro D21 Foxo3dNES Tg oocyte cultured under normoxia


title: vitro_Foxo3dNES_Tg_D21_Normoxia_rep1


title: vitro_Foxo3dNES_Tg_D21_rep1

source_name: In vitro D21 Foxo3dNES Tg oocyte


title: vitro_Foxo3dNES_Tg_D21_rep2


title: vitro_WT_D21_Normoxia_rep2

source_name: In vitro D21 WT oocyte cultured under normoxia


title: vitro_WT_D21_Normoxia_rep1


title: vitro_WT_D21_rep1

source_name: In vitro D21 WT oocyte


title: vitro_D20_rep3

source_name: In vitro D20 oocyte


title: vitro_D17_rep2

source_name: In vitro D17 oocyte


title: vitro_D20_rep1


title: vitro_D15_rep1

source_name: In vitro D15 oocyte


title: vitro_D15_rep3


title: vitro_D13_rep2

source_name: In vitro D13 oocyte


title: vitro_D15_rep2


title: IGF1_0h_Rep4


title: IGF1_0h_Rep1


title: vitro_D20_rep2


title: vitro_D17_rep3


title: vitro_D11_rep2

source_name: In vitro D11 germ cell

value: Germ cell


title: vitro_D10_rep3

source_name: In vitro D10 germ cell


title: vitro_D17_rep1


title: vitro_D10_rep2


title: vitro_D11_rep1


title: vitro_D10_rep1


title: vitro_D9_rep3

source_name: In vitro D9 germ cell


title: vitro_D9_rep2


title: vitro_WT_D21_rep2


title: vitro_D13_rep3


title: vitro_D9_rep1


title: vitro_D7_rep2

source_name: In vitro D7 germ cell


title: vitro_D7_rep3


title: vitro_D13_rep1


title: vitro_D7_rep1


title: vitro_D5_rep3

source_name: In vitro D5 germ cell


title: vitro_D5_rep2


title: vitro_D11_rep3


title: vitro_D5_rep1


title: vivo_P4_small_rep1

source_name: In vivo P4 small oocyte

value: C57BL/6 x B6D2F1


title: vivo_P4_large_rep1

source_name: In vivo P4 large oocyte


title: vivo_P4_large_rep2


title: vivo_P4_large_rep3


title: vivo_P4_small_rep3


title: vivo_P4_small_rep2


title: WT MEF IFNb rep3

city: Vienna

first: Ekaterini

last: Platanitis

address: Dr.-Bohr-Gasse 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: University of Vienna

description: IFNb treatment

data_processing:
Reads mapping to mouse rRNA transcripts were removed using bwa/0.7.12 alignment and samtools/1.3.1. Remaining reads were aligned to Mus musculus genome mm10 using TopHat v2.1.1 (GTF annotation file mm10, RefSeq from UCSC, 2015/02). Reads in genes were counted with htseq-count v0.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) supplemented with 10% of fetal calf serum (FCS) (Sigma-Aldrich), and 100 units/ml penicillin, and 100 ng/ml streptomycin (Sigma-Aldrich). Cells were kept at 37°C and 5% CO2.

extract_protocol:
Cells were washed twice with cold PBS. For total RNA isolation, 4 ml Qiazol Lysis Reagent (Qiagen) were added per 15 cm dish. 1ml of the ysate was used for RNA isolation. For DNase treatment and clean up the RNase-free DNase Set (Qiagen, #79254) and RNeasy Mini Kit (Qiagen, #74104) were used.
For library preparation, the NEBNext® Poly(A) mRNA Magnetic Isolation Module together with the NEBNext Ultra II RNA Library Prep Kit from NEB #E7770L was used according to the manufacturer’s protocol. The RNA quality was assessed using Agilent RNA 6000 Nano Assays that were analyzed on an Agilent 2100 Bioanalyzer and all samples displayed a RIN>9.

treatment_protocol: MEFs were seeded to 90 % confluency on 15 cm dishes, respectively. The next day cells were stimulated for 2h with 250 IU/mL of IFNβ (PBL interferon source).

value: wildtype


title: WT MEF rep3


title: WT MEF rep2


title: IRF9KO MEF rep2


title: WT MEF IFNb rep2

description: IFNb treatment


title: IRF9KO MEF rep3


title: WT MEF IFNb rep1

description: IFNb treatment


title: IRF9KO MEF IFNb rep3

description: IFNb treatment


title: IRF9KO MEF IFNb rep2

description: IFNb treatment


title: IRF9KO MEF rep1


title: WT MEF rep1


title: WT MEF STAT2

data_processing:
Raw reads were aligned to the mouse mm10 genome (bowtie2; v2.2.9; default settings; mm10 iGenomes); the aligned bam files were filtered to remove reads with low mapping quality (samtools; v1.4; -q 10), overlap with ENCODE blacklisted regions (bedtools; v.25.0; intersectBed) and duplicates (picard; v2.1.1; MarkDuplicates), and used to generate bigiwig files (deeptools; v3.1.1; bamCoverage; --normalizeUsing RPGC --binSize 10 --extendReads 200)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file of RPGC normalized read coverages

extract_protocol:
Cells were washed 2x with ice cold PBS and crosslinked for 10 minutes at room temperature in 1% formaldehyde PBS (thermos fischer #28906). The cross-linked chromatin was sheared by sonication, providing fragments of 200 - 1400 base pairs in length.Protein-DNA complexes were selectively immunoprecipitated using STAT1,STAT2 and IRF9 antibodies. The immunoprecipitated complexes were washed to remove non-specifically bound chromatin, the protein-DNA cross-link was reversed and proteins were removed by proteinase K digest. Four IPs were pooled for each sample, in order to obtain enough DNA precipitated.  The DNA associated with the complex was furthermore purified and used for ChIP-seq.
For library generation, the NEBNext Ultra II DNA Library Prep Kit for Illumina from NEB was used according to the manufacturer's protocol. The chromatin quality was analyzed on an Agilent 2100 Bioanalyzer and a size selection of 200-1400bp was carried out.

tag: antibodies

value: Stat2 (L-20) Santa Cruz sc-950, RRID:AB_2271322


title: WT MEF STAT1

value: Stat1 (E23) Santa Cruz sc-346, RRID:AB_632435


title: IRF9KO 2h IFNg rep2

source_name: IRF9KO 2h IFNg, BMDM

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from bone marrow isolated from femurs and tibias of 8- to 10-week-old mice. Femur and tibia were separated by cutting at the knee joint. Bones were flushed with Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) using a 5-mL syringe and a 25-gauge needle. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) supplemented with 10% of fetal calf serum (FCS) (Sigma-Aldrich), recombinant M-CSF, 100 units/ml penicillin, and 100 ng/ml streptomycin (Sigma-Aldrich). Cells were kept at 37°C and 5% CO2 and differentiated for 10 days.

extract_protocol:
Cells were washed twice with cold PBS. For total RNA isolation, 7 ml Qiazol Lysis Reagent (Qiagen) were added per 15 cm dish. 1ml of the ysate was used for RNA isolation. For DNase treatment and clean up the RNase-free DNase Set (Qiagen, #79254) and RNeasy Mini Kit (Qiagen, #74104) were used.
For library preparation, the NEBNext® Poly(A) mRNA Magnetic Isolation Module together with the NEBNext Ultra II RNA Library Prep Kit from NEB #E7770L was used according to the manufacturer’s protocol. The RNA quality was assessed using Agilent RNA 6000 Nano Assays that were analyzed on an Agilent 2100 Bioanalyzer and all samples displayed a RIN>9.

treatment_protocol: 1.5 x 10^7 cells were seeded with 90 % confluency on 15 cm dishes, respectively. The next day cells were stimulated for 2h either with with 10 ng/ml murine interferon gamma (IFN-γ; eBioscience) or 250 IU/mL of IFNβ (PBL interferon source).

value: 8-10 weeks

tag: treatment

value: IFNg

value: bone marrow derived macrophages


title: IRF9KO 2h IFNg rep3


title: WT MEF IRF9

value: IRF9 clone 6F1 homemade


title: WT MEF IRF9 90 min IFNb

description: 90 min IFNb treatment


title: WT MEF STAT1 90 min IFNb

description: 90 min IFNb treatment


title: WT MEF STAT2 90 min IFNb

description: 90 min IFNb treatment


title: IRF9KO 2h IFNb rep2

source_name: IRF9KO 2h IFNb, BMDM

value: IFNb


title: IRF9KO 2h IFNb rep3


title: IRF9KO 2h IFNg rep1


title: IRF9KO rep3

source_name: IRF9KO, BMDM

value: untreated


title: IRF9KO rep2


title: WT 2h IFNg rep3

source_name: WT 2h IFNg, BMDM


title: IRF9KO 2h IFNb rep1


title: VPA day50-56 Rep3

source_name: hES-iN_VPA day50-56

value: hES derived induced neurons (hES-iN)

value: Valproic acid


title: WT 2h IFNb rep2

source_name: WT 2h IFNb, BMDM


title: WT 2h IFNg rep2


title: IRF9KO MEF IFNb rep1

description: IFNb treatment


title: VPA day50-56 Rep2


title: WT 2h IFNg rep1


title: WT 2h IFNb rep1


title: WT 2h IFNb rep3


title: WT rep3

source_name: WT, BMDM


title: VPA day50-56 Rep1


title: WT rep2


title: IRF9KO rep1


title: Ctrl day50-56 Rep3

source_name: hES-iN_Ctrl day50-56

value: control


title: WT rep1


title: Ctrl day50-56 Rep2


title: Ctrl day50-56 Rep1


title: VPA day1 Rep4

source_name: hES-iN_VPA day4


title: IRF9KO STAT1 90 min IFNg rep2

data_processing:
Raw reads were processed using the AQUAS TF pipeline (https://github.com/kundajelab/chipseq_pipeline;based off Encode phase-3;-idr_thresh 0.01): including alignment against the Mus musculus mm10 genome using BWA (v0.7.13), deduplication using Picard MarkDuplicates (v1.126), Peak Calling using macs2 (v2.1.1) and spp (v1.13).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak formatted peak sets for each replicate as called by macs2;  narrowPeak formatted optimal peak sets for each condition using SPP peak calling for both replicates and combined using idr analysis (idr_threshold 0.01)

source_name: IRF9KO STAT1 90 min IFNg, BMDM

extract_protocol:
Cells were washed 2x with ice cold PBS and crosslinked for 10 minutes at room temperature in 1% formaldehyde PBS (thermos fischer #28906). The cross-linked chromatin was sheared by sonication, providing fragments of 200 - 1400 base pairs in length.Protein-DNA complexes were selectively immunoprecipitated using STAT1,STAT2 and IRF9 antibodies. The immunoprecipitated complexes were washed to remove non-specifically bound chromatin, the protein-DNA cross-link was reversed and proteins were removed by proteinase K digest. Four IPs were pooled for each sample of the two biological replicates, in order to obtain enough DNA precipitated.  The DNA associated with the complex was furthermore purified and used for ChIP-seq.
For library generation, the NEBNext Ultra II DNA Library Prep Kit for Illumina from NEB was used according to the manufacturer’s protocol. The chromatin quality was analyzed on an Agilent 2100 Bioanalyzer and a size selection of 200-1400bp was carried out.

treatment_protocol: 1.5 x 10^7 cells were seeded with 90 % confluency on 15 cm dishes, respectively. The next day cells were stimulated for 90 minutes either with with 10 ng/ml murine interferon gamma (IFN-γ; eBioscience) or 250 IU/mL of IFNβ (PBL interferon source).

tag: chip antibody


title: IRF9KO STAT2 90 min IFNg rep2

source_name: IRF9KO STAT2 90 min IFNg, BMDM


title: IRF9KO STAT1 90 min IFNg rep1


title: VHL vs WT replicate 2

city: Bologna

first: Giuseppe

last: Gargiulo

address: Via Selmi, 3

country: Italy

institute: University of Bologna

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

label_protocol: Adjust RNA volume to 3 µL with DEPC-water and add 1 µL 3'-SMART CDS Primer IIA (10 µM) and 1 µL SMART IIA chimeric oligo (10 µM). Incubate at 70 °C for 5 minutes, then snap cool on ice. Add 2 µl 5x First Strand Buffer (Invitrogen), 0.5 µL 0.1M DTT (Invitrogen), 0.5 µL 10 mM dNTP mix and 1 µl 200 U/µL Superscript III (Invitrogen). Incubate at 46 °C for 1.5 hours, then cool on ice (store samples at 4 °C or -20 °C). To determine the optimal number of cycles required for generating products in exponential phase, 2 µL of the PCR products from a parallel run are visualised at every second cycle from cycle 14 to 26 on 1% agarose gel using one reaction of each sample type. To 5 µL of the first-strand reaction (include negative and positive controls) add 5 µL 10x Advantage II PCR buffer (Clontech), 1 µL 10 mM dNTP mix, 2 µL 20 µM 5' PCR Primer II, 1 µL 50x Advantage II Polymerase Mix (Clontech) and adjust volume to 50 µL with DEPC-water. Run PCR program: step 1: 95 °C - 1 min, step 2: 95 °C - 5 sec, step 3: 65 °C - 5 sec, step 4: 68 °C - 6 min, cycle from step 2 for 27 more times. Run PCR aliquots on 1% agarose gel and select cycle number below saturation. Then perform amplification using the optimal number of 18 cycles on the remaining 5 µL of the first-strand reaction. Purify PCR products using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).  SMART II A chimeric primer: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CGC-888-3'  (8 = riboG)  3' SMART CDS Primer IIA: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GTA-CTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-TTT-VN-3' (V = G+A+C, N = A+C+G+T)  5' PCR Primer II: 5'-AAG-CAG-TGG-TAT-CAA-CGC-AGA-GT-3'

growth_protocol: Flies were aged at 25°C. 5 days old yw and dVHL+/- 0 Drosophila female Malpighian tubules were collected at 20°C.

extract_protocol: Homogenise tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle and add up to 700 µl of TRIzol. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes at 4 °C to pellet debris. Transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, shake vigorously for 15 seconds and incubate at room temperature for 2-3 minutes. Centrifuge at 13,000 rpm for 15 minutes at 4 °C. Transfer upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.7 volumes of isopropanol to precipitate the RNA. Incubate at room temperature for 5 minutes or 1 hour at -20 °C and then centrifuge at 13,000 rpm for 15 minutes at 4 °C. Discard the supernatant and wash the RNA pellet with 1 ml 70% ethanol/DEPC MilliQ water. Centrifuge at 13,000 rpm for 10 minute at 4 °C. Air-dry the pellet briefly (~ 5 minutes). Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 20 to 50 µl. The RNA will dissolve more readily if the DEPC MilliQ water is preheated to 55 °C. Verify quality of RNA on a 1 % agarose gel and quantify with a Nanodrop.

treatment_protocol: Female were anesthetized by using CO2, put on a slide and dissected in PBS under the dissecting microscope. Malpighian tubules were then placed on ice in the Trizol solution.

tag: developmental stage

value: 5 days old adult

tag: gender

value: Female


title: VHL vs WT replicate 3

description: dye swap


title: VPA day1 Rep2


title: Photo-aged skin 7 days post Fraxel, Rep_14

city: Baltimore

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Gene expression data from human arm with or without laser treatment.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RNA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: female human arm skin biopsy

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

extract_protocol: 7 days after laser treatment, arm skin was biopsied for total RNA isolation from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Arm skin was treated with Fraxel CO2 laser once, control skin was not treated.

value: Arm skin

value: CO2 laser (Fraxel)


title: VPA day1 Rep1


title: Photo-aged skin 7 days post Fraxel, Rep_16


title: Photo-aged skin 7 days post Fraxel, Rep_12


title: VHL vs WT replicate 4

description: dye swap


title: IRF9KO STAT2 90 min IFNb rep2

source_name: IRF9KO STAT2 90 min IFNb, BMDM

tag: strain


title: Photo-aged skin 7 days post Fraxel, Rep_15


title: VPA day1 Rep3


title: Photo-aged skin 7 days post Fraxel, Rep_11


title: Ctrl day1 Rep4

source_name: hES-iN_Ctrl day4


title: Photo-aged skin 7 days post Fraxel, Rep_6


title: Photo-aged skin 7 days post Fraxel, Rep_9


title: Photo-aged skin 7 days post Fraxel, Rep_10


title: VHL vs WT replicate 1


title: Photo-aged skin 7 days post Fraxel, Rep_5


title: Photo-aged skin 7 days post Fraxel, Rep_13


title: Photo-aged skin 7 days post Fraxel, Rep_7


title: Photo-aged skin 7 days post Fraxel, Rep_4


title: Photo-aged skin 7 days post Fraxel, Rep_1


title: Photo-aged skin 7 days post Fraxel, Rep_3


title: Photo-aged skin 7 days post Fraxel, Rep_2


title: Photo-aged skin 7 days post Fraxel, Rep_8


title: IRF9KO STAT2 90 min IFNg rep1


title: IRF9KO STAT1 90 min IFNb rep2

source_name: IRF9KO STAT1 90 min IFNb, BMDM


title: IRF9KO STAT2 90 min IFNb rep1


title: Ctrl day1 Rep3


title: Photo-aged skin pre-treatment base line control, Rep_14

value: Untreated


title: Ctrl day1 Rep2


title: IRF9KO STAT2 rep2

source_name: IRF9KO STAT2, BMDM


title: Ctrl day1 Rep1


title: IRF9KO STAT1 rep2

source_name: IRF9KO STAT1, BMDM


title: WT THP rep3

data_processing:
Reads mapping to human rRNA transcripts were removed using bwa/0.7.12 alignment and samtools/1.3.1. Remaining reads were aligned to human genome hg38 using TopHat v2.1.1 (GTF annotation file hg38, RefSeq from UCSC, 2015/01). Reads in genes were counted with htseq-count v0.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

source_name: Human monocytic THP1

growth_protocol: Human monocytic THP1 were maintained in RPMI 1640 culture medium (Sigma-Aldrich) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Sigma-Aldrich) and 1% Penicillin/Streptomycin (both Sigma-Aldrich).Cells were kept at 37°C and 5% CO2.

treatment_protocol: 1,5x10^7 Human monocytic THP1 were seeded on a 15 cm dish and differentiated into macrophage-like cells by treating them with 100nM phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) in complete media for 48 hours at 37°C and 5% CO2 atmosphere. On the third day, media containing 100nM PMA was changed to RPMI 1640 media exclusively supplemented with 10% FBS (containing neither PMA nor antibiotics) and incubation at 37°C and 5% CO2 atmosphere was continued for additional 24 hours. The next day cells were stimulated for 2h with 250 IU/mL of IFNβ (PBL interferon source).

value: wildtype


title: IRF9KO STAT2 rep1

value: Stat2 (L-20) Santa Cruz sc-950, RRID:AB_2271322


title: input_DNA

data_processing:
reads are filtered and trimed with Cutadapt
reads are aligned to genome using Bowtie2
MACS2 is used for peak calling
Differential binding in CHIP-seq was performed with DESeq2 package in r.
Genome_build: hg19 and mm10

extract_protocol:
Cells are fixed, washed, and lysed to purify the nuceli. Then chromatin were fragmented with Covaris, and mixed with antibody and beads to pull down the bound fraction as described in the manuscript
Standard CHIP-seq libraries made using NEBnext Ultra II kit from chipped DNA

value: human mammary gland epithelial cell line


title: Photo-aged skin pre-treatment base line control, Rep_13


title: Photo-aged skin pre-treatment base line control, Rep_12


title: WT THP rep2


title: WT THP rep1


title: Photo-aged skin pre-treatment base line control, Rep_11


title: MCF10A_N_terminal

source_name: MCF10A expressing satb1 fusion

value: expressing N-terminal domain of Satb1

value: Anti-GFP antibody (Abcam, Ab290)


title: Photo-aged skin pre-treatment base line control, Rep_7


title: WT IRF9 90 min IFNg rep2

source_name: WT IRF9 90 min IFNg, BMDM

value: 8-10 weeks

value: IFNg

value: bone marrow derived macrophages


title: IRF9KO STAT1 rep1

value: untreated

value: Stat1 (E23) Santa Cruz sc-346, RRID:AB_632435


title: Photo-aged skin pre-treatment base line control, Rep_9


title: Photo-aged skin pre-treatment base line control, Rep_16


title: MCF10A_NC1_CHIP_seq

value: expressing Satb1 N terminal domain and CUT1 domain


title: Photo-aged skin pre-treatment base line control, Rep_8


title: Photo-aged skin pre-treatment base line control, Rep_10


title: IRF9KO STAT1 90 min IFNb rep1

value: IFNb


title: MCF10A_deltaHD_CHIP_seq

value: expressing Satb1 without homeodomain (HD)


title: WT IRF9 90 min IFNg rep1

value: IRF9 clone 6F1 homemade


title: WT THP IFNb rep3

description: IFNb treatment


title: WT THP IFNb rep2

description: IFNb treatment


title: MCF10A_satb1_CHIP_seq

value: expressing Satb1 full length protein


title: WT STAT2 90 min IFNg rep2

source_name: WT STAT2 90 min IFNg, BMDM


title: WT THP IFNb rep1

description: IFNb treatment


title: WT STAT2 90 min IFNg rep1


title: Upf3_1_PARCLIP

city: Goettingen

first: Katharina

middle: Bettina

last: Hofmann

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
Library strategy: PAR-CLIP
Adapter sequences are trimmed and a quality filter discards reads containing unidentified nucleotides (N), Phred scores below 20, or reads shorter than 20
High-quality reads are aligned to S. cerevisiae genome (sacCer3, version 64.1.1) using Bowtie (v1.2). Reads are mapped uniquely with a maximum of one tolerated mismatch
Mockinbird is used for statistical evaluation of binding sites. A p-value threshold of 0.005 was set as well as the minimum coverage of 2 per site.
Genome_build: S. cerevisiae genome (sacCer3, version 64.1.1)
Supplementary_files_format_and_content: tab delimited text files containing verified cross-link sites (p-value<0.005), their genomic locations, p-values and occupancies

organism: Saccharomyces cerevisiae

source_name: Yeast cell extract

growth_protocol: 4tU-labeled yeast cells (BY4741) expressing C-terminally TAP-tagged protein were UV-irradiated with an energy dose of 10-12 J/cm2 at 365 nm.

extract_protocol:
The cells were lysed by bead beating and IP was performed with rabbit IgG-conjugated protein G magnetic Dynabeads (Invitrogen). The cross-linked RNA was partially digested with RNase T1 (Thermo Scientific) and the IP was controlled by performing a western blot analysis of a part of the sample using the Peroxidase Anti-Peroxidase (PAP; Sigma) antibody. Following adapter ligation, RNA was recovered by digestion with proteinase K (New England Biolabs) and a subsequent acidic phenol/chloroform extraction.
Reverse transcription was performed with SuperScript III RTase (Invitrogen) and was followed by PCR amplification using the NEXTflex barcode primer kit (Bio Scientific). The generated cDNA was purified, size selected, and quantified using TapeStation (Agilent Technologies). The resulting samples were then PCR-amplified and sequenced on an Illumina HiSeq 1500, HiSeq2500 or NextSeq550 system.

treatment_protocol: 1 mM 4tU for 4 h.

tag: strain background

tag: degradation factor


title: WT STAT1 90 min IFNg rep2

source_name: WT STAT1 90 min IFNg, BMDM


title: Upf2_1_PARCLIP


title: Trf5_1_PARCLIP


title: Trf4_1_PARCLIP


title: Photo-aged skin pre-treatment base line control, Rep_4

value: Arm skin

tag: Sex

value: Female


title: Photo-aged skin pre-treatment base line control, Rep_3

value: Untreated


title: WT IRF9 90 min IFNb rep2

source_name: WT IRF9 90 min IFNb, BMDM

value: wildtype


title: IRF9KO THP rep2


title: IRF9KO THP rep3


title: WT STAT1 90 min IFNg rep1


title: IRF9KO THP rep1


title: Upf1_1_PARCLIP


title: WT IRF9 90 min IFNb rep1


title: Rrp44_1_PARCLIP


title: Photo-aged skin pre-treatment base line control, Rep_2


title: IRF9KO THP IFNb rep3

description: IFNb treatment


title: Photo-aged skin pre-treatment base line control, Rep_6


title: Photo-aged skin pre-treatment base line control, Rep_5


title: Ski8_1_PARCLIP


title: Pan3_1_PARCLIP


title: Ski7_1_PARCLIP


title: IRF9KO THP IFNb rep2

description: IFNb treatment


title: Ski2_1_PARCLIP


title: Photo-aged skin pre-treatment base line control, Rep_1


title: Ski3_1_PARCLIP


title: Pan2_1_PARCLIP


title: IRF9KO THP IFNb rep1

description: IFNb treatment


title: WT STAT2 90 min IFNb rep1

source_name: WT STAT2 90 min IFNb, BMDM

value: Stat2 (L-20) Santa Cruz sc-950, RRID:AB_2271322


title: Rrp6_1_PARCLIP


title: Rrp40_1_PARCLIP


title: WT THP STAT2

data_processing:
Raw reads were aligned to the human hg38 genome (bowtie2; v2.2.9; default settings; hg38 iGenomes); the aligned bam files were filtered to remove reads with low mapping quality (samtools; v1.4; -q 10), overlap with ENCODE blacklisted regions (bedtools; v.25.0; intersectBed) and duplicates (picard; v2.1.1; MarkDuplicates), and used to generate bigiwig files (deeptools; v3.1.1; bamCoverage; --normalizeUsing RPGC --binSize 10 --extendReads 200)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig file of RPGC normalized read coverages

source_name: human monocytic THP1

treatment_protocol: 1,5x10^7 Human monocytic THP1 were seeded on a 15 cm dish and differentiated into macrophage-like cells by treating them with 100nM phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich) in complete media for 48 hours at 37°C and 5% CO2 atmosphere. On the third day, media containing 100nM PMA was changed to RPMI 1640 media exclusively supplemented with 10% FBS (containing neither PMA nor antibiotics) and incubation at 37°C and 5% CO2 atmosphere was continued for additional 24 hours. The next day cells were stimulated for 90min with 250 IU/mL of IFNβ (PBL interferon source).

value: Stat2 (D9J7L) Cell Signaling Technology Cat#72604


title: WT STAT1 90 min IFNb rep2

source_name: WT STAT1 90 min IFNb, BMDM


title: WT THP STAT2 IFNb

description: 90 min IFNb treatment


title: WT THP STAT1

value: Stat1 (D4Y6Z) Cell Signaling Technology Cat# 14995, RRID:AB_2716280


title: Rrp4_1_PARCLIP


title: WT STAT2 90 min IFNb rep2

value: 8-10 weeks


title: Pop2_1_PARCLIP


title: WT THP IRF9

value: IRF9 (D2T8M) Cell Signaling Technology Cat# 76684


title: Dcp2_1_PARCLIP


title: Not1_1_PARCLIP


title: Nmd4_1_PARCLIP


title: Dcp1_1_PARCLIP


title: WT STAT1 90 min IFNb rep1

value: bone marrow derived macrophages


title: WT STAT2 rep2

source_name: WT STAT2, BMDM

value: untreated


title: Edc2_1_PARCLIP


title: Dhh1_1_PARCLIP


title: WT IRF9 rep1

source_name: WT IRF9, BMDM


title: WT THP STAT1 IFNb

description: 90 min IFNb treatment


title: WT IRF9 rep2


title: Xrn1_1_PARCLIP


title: Air1_1_PARCLIP


title: ATB

city: Beijing

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

data_processing:
The clean small RNA reads were mapped to human reference genome (hg38) by Bowtie.
We first identified known miRNAs based on miRBase20.0 (miRBase, http://www.mirbase.org/).
Then we used miRDeep2 to predict new miRNAs.
Expression were quantified by transcript per million (TPM). Differential expression was determined using DEGseq R package.
Genome_build: hg38
Supplementary_files_format_and_content: txt file include TPM, fold change and p-value for each miRNAs and each sample in the related statistical test.

source_name: serum exosomes

extract_protocol:
We isolated the serum exosomes as previously described (Lv et al., 2017). We first performed differential centrifugation (1000 g for 10 min at 4 °C, and 16,500 g for 30 min at 4 °C) to remove the cell debris, followed by ultrafiltration using 0.22 μm filters. We then performed ultracentrifugation (120,000 g for 2 hours) to obtain exosome pellets. Transmission electron microscopy (TEM) was employed to visualize exosomes. The exosome pellets were first suspended and dropped onto 200 mesh copper grids, followed by incubation in 3% phosphotungstic acid for 10 min. The copper mesh was then washed three times with water and dried for observation by TEM. We also analyzed the exosome size distributions using the nanoparticle tracking analysis (NTA, Malvern, UK) according to the manufacturer’s instructions.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: serum exosomes

tag: condition

value: active tuberculosis patients


title: Mtr4_1_PARCLIP


title: Csl4_1_PARCLIP


title: Ccr4_1_PARCLIP


title: Edc3_1_PARCLIP


title: WT STAT1 rep1

source_name: WT STAT1, BMDM

value: Stat1 (E23) Santa Cruz sc-346, RRID:AB_632435

tag: cell type


title: Caf40_1_PARCLIP


title: WT THP IRF9 IFNb

description: 90 min IFNb treatment


title: LTBI

value: latent tuberculosis infection


title: Air2_1_PARCLIP


title: WT STAT2 rep1


title: input

source_name: input, BMDM


title: WT STAT1 rep2


title: HC

value: healthy control


title: PD

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

data_processing:
Illumina Casava 1.8+ software used for basecalling.
sRNA libraries were sequenced using the Illumina Genome Analyzer. Raw data of fastq format were firstly processed through custom perl and python scripts.
NGS QC Toolkit v2.3.3 was used to filiter the reads with adapter sequences, reads with an N (unknown bases in a read＞5%) and low-quality reads (reads with a base quality ≤ 20).
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze the expression and distribution on the reference genome.The mapped sRNA tags were also mapped to miRBase22.0, Rfam, siRNA, piRNA, snoRNA to annotate the tags and remove those originating from proteincoding genes, ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs). Custom scripts were used to obtain the miRNA counts. The remaining unannotated tags were used to predict novel miRNAs by exploring secondary structures, Dicer cleavage sites, and minimum free energies using RIPmiR software packages. MiRNA expression was normalized by transcripts per million (TPM) ('t Hoen et al. 2008)
Target genes were predicted by both TargetFinder and psRobot according to the default parameters.
Genome_build: GigaScience GigaDB   (http://gigadb.org/dataset/100209, Guan et al. 2016).
Supplementary_files_format_and_content: Text files include PD_miRNA (miRNA_id, Count, TPM, Mature_sequence) and miRNA_target (miRNA_id, target_id)

organism: Ginkgo biloba

source_name: ovular secretion

growth_protocol: Ovular secretions were obtained from the ovule of female G. biloba trees

extract_protocol:
Samples were collected in April 2017. Total RNAs of ovular secretions were extracted using modified CTAB method.
sRNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ location

value: mature ovule (secretory phase)


title: CD19negCD22neg non-B cells from TONS01

status: Public on May 27 2019

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

country: France

institute: Rennes University Hospital

description: Cells were purified using magnetic beads

hyb_protocol: Following fragmentation, cARN were hybridized on GeneChip Human U133Plus2.0 arrays

scan_protocol: GeneChips were scanned using the Genechip Scanner Affymetrix

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC). Normalization was performed by  the GC-RMA algorithm using the Partek Genomics Suite software (Partek, St Louis, MO). Dataset was then filtering by eliminating PS with no expression in all dataset and/or no gene symbol annotations.

source_name: non-B cells purified from reactive non tumoral tonsil

label_protocol: Biotinylated cRNA were amplified according to the small sample labeling protocol (Affymetrix, Santa Clara, CA)

extract_protocol: RNA extraction was performed using Allprep ARN/ADN mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions, including DNASe I treatment.

treatment_protocol: Purification of B (CD19pos) and non-B (CD19negCD22neg) fractions was performed using a two-step magnetic bead cell sorting. First, CD19pos B lymphocytes were obtained by positive selection using CD19 microbeads (StemCell Technologies, Vancouver, Canada). Residual B cells were then eliminated from the unbound fraction by a second round of depletion using CD22 microbeads (Miltenyi Biotec, Gladach, Germany), obtaining, therefore, the CD19negCD22neg microenvironment compartment (Env)

tag: diagnosis

value: Healthy donor

tag: tissue

value: Tonsil

value: CD19negCD22neg non-B cells (ENV)


title: CD19negCD22neg non-B cells from TONS03


title: CD19negCD22neg non-B cells from TONS05


title: CD19negCD22neg non-B cells from RLN01

source_name: non-B cells purified from reactive non tumoral lymph node

value: Lymph node


title: CD19negCD22neg non-B cells from FL32

source_name: non-B cells purified from follicular lymphoma lymph node

value: FL patient


title: CD19negCD22neg non-B cells from FL29


title: CD19negCD22neg non-B cells from FL33


title: CD19negCD22neg non-B cells from RLN02


title: CD19negCD22neg non-B cells from TONS02


title: CD19negCD22neg non-B cells from TONS04


title: CD19negCD22neg non-B cells from RLN03


title: Photo-aged skin pre-treatment base line control, Rep_15

source_name: female human arm skin biopsy

value: Arm skin

value: Female

value: Untreated


title: CD19negCD22neg non-B cells from FL28


title: CD19negCD22neg non-B cells from FL17


title: CD19negCD22neg non-B cells from FL35


title: CD19negCD22neg non-B cells from FL13


title: CD19negCD22neg non-B cells from FL11


title: CD19negCD22neg non-B cells from RLN05


title: CD19negCD22neg non-B cells from FL10


title: CD19negCD22neg non-B cells from FL03


title: CD19negCD22neg non-B cells from FL02


title: CD19negCD22neg non-B cells from FL07


title: CD19negCD22neg non-B cells from FL08


title: CD19negCD22neg non-B cells from FL06


title: CD19negCD22neg non-B cells from RLN04


title: CD19negCD22neg non-B cells from RLN011


title: CD19pos lymphocytes from RLN09

source_name: B lymphocytes purified from reactive non tumoral lymph node

value: CD19pos B lymphocytes


title: CD19pos lymphocytes from RLN10


title: CD19pos lymphocytes from RLN11


title: CD19pos lymphocytes from RLN05


title: CD19pos lymphocytes from RLN01


title: CD19pos lymphocytes from FL07

source_name: B tumor cells purified from follicular lymphoma lymph node


title: CD19pos lymphocytes from FL28


title: CD19pos lymphocytes from RLN08


title: CD19pos lymphocytes from FL14


title: CD19pos lymphocytes from RLN03


title: CD19pos lymphocytes from RLN07


title: CD19pos lymphocytes from FL13


title: CD19pos lymphocytes from FL29


title: CD19pos lymphocytes from FL15


title: CD19pos lymphocytes from FL31


title: CD19pos lymphocytes from FL33


title: CD19pos lymphocytes from FL32


title: CD19pos lymphocytes from RLN06


title: CD19pos lymphocytes from FL08


title: CD19pos lymphocytes from FL17


title: CD19pos lymphocytes from FL04


title: CD19pos lymphocytes from FL09


title: CD19pos lymphocytes from FL30


title: CD19pos lymphocytes from FL12


title: CD19pos lymphocytes from FL11


title: CD19pos lymphocytes from RLN02


title: CD19pos lymphocytes from FL06


title: E775_Hand2_KO2

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens Street

department: Cardiovascular Disease

institute: J. David Gladstone Institutes

description:
Single cell transcriptomes from cardiac crescent region from E7.75 Hand2-null mouse embryo
processed data file #2: E775E825_WTKO_10X.csv.gz

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (2.0.1) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v2.2 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Each cell is identified by the barcode and gem.group ID at the end of the barcode in the processed data files (e.g. AAACCTGGTAAAGGAG-1). The gem.group ID for each sample and associated processed data file is provided in the characteristics fields above.
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene-cellbarcode expression matrix in csv format

source_name: Embryonic mouse heart at E7.75

growth_protocol: Timed matings were set up between mice heterozygous for the Hand2 null allele. Morning of plug detection was considered E0.5 and embryos were harvested at embryonic day (E)7.75, E8.25 or E9.25

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes and resuspended in 35ul of PBS/1% FBS

value: heart

tag: specific heart region

value: Cardiac Crescent region

tag: additional cell lineages present in dataset

value: Non-cardiac mesoderm, ectoderm and endoderm

tag: gem.group in supplementary file # 2


title: CD19pos lymphocytes from FL01


title: CD19pos lymphocytes from FL03


title: CD19pos lymphocytes from FL16


title: CD19pos lymphocytes from FL10


title: E775_Hand2_KO3

tag: genotype


title: E775_Hand2_KO1


title: E775_WT2

description:
Single cell transcriptomes from cardiac crescent region from E7.75 WT mouse embryo
processed data file #1: AllTimePoints_WT_10X.csv.gz
processed data file #2: E775E825_WTKO_10X.csv.gz

value: Wild-Type

tag: gem.group id in supplementary file # 1


title: E775_WT4


title: E775_WT5


title: E775_WT3


title: E775_WT1


title: SLX-16202.i729_i521

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

data_processing:
Download ERCC sequences from Thermofisher (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt) and append them to mouse genome
Create star index using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49 --genomeFastaFiles /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/GRCm38.p6.all.ERCC.fa --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf --sjdbOverhang 49`
Perform alignment using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49/ --readFilesIn /scratch/rulands/Liver_Embryo_Meri_Huch/fastq --readFilesCommand zcat --outFileNamePrefix /scratch/rulands/Liver_Embryo_Meri_Huch/aligned_reads/ --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf`
Generate count matrix using subread 1.6.2. Command: `~/bin/subread-1.6.2-Linux-x86_64/bin/featureCounts -T 10 -t exon -g gene_id -a /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf -Q 30 -o counts.csv *.bam`; sed 1d counts.csv | cut -f1,7- | sed s/Geneid/id/ > counts_final_ercc.txt
Reading count matrix from `counts_final_ercc.txt` and metadata into scanpy 1.3.3 (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Quality control on cells (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Normalisation using scran (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Batch effect correction using mnn_correct (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Genome_build: Ensemble GRCm38, release 93
Supplementary_files_format_and_content: raw count and normalized counts

source_name: E10.5_liver_Lgr5GFP pos

extract_protocol:
E10.5 and E13.5 mouse livers were collected, digested into single cells and sorted by FACS to isolate Lgr5-GFP positive cells or bulk liver cells from each timepoint.
The Illumina Nextera XT DNA preparation kit (FC-131-1096) was used to prepare libraries.

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

tag: embryonic day

value: liver hepatoblast cells

tag: sorting

value: Lgr5GFP pos


title: CD19pos lymphocytes from FL02


title: SLX-16202.i729_i516

value: Bulk


title: CD19pos lymphocytes from FL34


title: SLX-16202.i729_i520


title: SLX-16202.i728_i520


title: SLX-16202.i729_i518


title: SLX-16202.i729_i517


title: SLX-16202.i729_i515


title: SLX-16202.i728_i516


title: SLX-16202.i728_i518


title: SLX-16202.i728_i515


title: SLX-16202.i728_i517


title: SLX-16202.i728_i513


title: SLX-16202.i727_i522


title: SLX-16202.i728_i522


title: SLX-16202.i728_i521


title: SLX-16202.i727_i521


title: SLX-16202.i727_i520


title: SLX-16202.i727_i517


title: SLX-16202.i727_i518


title: SLX-16202.i727_i515


title: SLX-16202.i727_i516


title: SLX-16202.i726_i518


title: SLX-16202.i726_i521


title: SLX-16202.i726_i522


title: SLX-16202.i726_i520


title: SLX-16202.i726_i515


title: SLX-16202.i724_i522


title: SLX-16202.i726_i513


title: SLX-16202.i724_i520


title: SLX-16202.i724_i517


title: SLX-16202.i724_i516


title: SLX-16202.i724_i521


title: SLX-16202.i724_i515


title: SLX-16202.i724_i513


title: SLX-16202.i723_i518


title: SLX-16202.i723_i520


title: SLX-16202.i723_i517


title: SLX-16202.i723_i516


title: SLX-16202.i723_i515


title: SLX-16202.i723_i513


title: SLX-16202.i722_i521

source_name: E13.5_liver_Lgr5GFP pos


title: SLX-16202.i726_i516


title: SLX-16202.i727_i513


title: SLX-16202.i722_i515


title: SLX-16202.i726_i517


title: SLX-16202.i721_i517


title: SLX-16202.i721_i516


title: SLX-16202.i721_i515


title: SLX-16202.i719_i517


title: SLX-16202.i719_i516


title: SLX-16202.i720_i516


title: SLX-16202.i721_i518


title: SLX-16202.i719_i513


title: SLX-16202.i722_i513


title: SLX-16202.i719_i522


title: SLX-16202.i720_i515


title: SLX-16202.i718_i517


title: SLX-16202.i718_i521


title: SLX-16202.i718_i518


title: SLX-16202.i718_i516


title: SLX-16202.i716_i522


title: SLX-16202.i716_i516


title: SLX-16202.i715_i511


title: SLX-16202.i716_i515


title: SLX-16202.i715_i510


title: SLX-16202.i715_i505


title: SLX-16202.i714_i503


title: SLX-16202.i714_i505


title: SLX-16202.i714_i511


title: SLX-16202.i715_i508


title: SLX-16202.i712_i511


title: SLX-16202.i718_i522


title: SLX-16202.i712_i510


title: SLX-16202.i712_i508


title: SLX-16202.i712_i507


title: SLX-16202.i712_i505


title: SLX-16202.i711_i510


title: SLX-16202.i711_i506


title: SLX-16202.i712_i502


title: SLX-16202.i711_i511


title: SLX-16202.i711_i507


title: SLX-16202.i711_i508


title: SLX-16202.i707_i510


title: SLX-16202.i710_i508


title: SLX-16202.i710_i502


title: SLX-16202.i710_i510


title: SLX-16202.i711_i503


title: SLX-16202.i715_i506


title: SLX-16202.i707_i506


title: SLX-16202.i707_i508


title: SLX-16202.i714_i502


title: SLX-16202.i707_i503


title: SLX-16202.i707_i502


title: SLX-16202.i705_i505


title: SLX-16202.i704_i505


title: SLX-16202.i706_i503


title: SLX-16202.i705_i502


title: SLX-16202.i703_i506


title: SLX-16202.i704_i502


title: SLX-16202.i702_i505


title: SLX-16202.i710_i507


title: SLX-16202.i710_i511


title: SLX-16202.i701_i505


title: SLX-16202.i701_i503


title: SLX-14713.i729_i506


title: SLX-14713.i729_i503


title: SLX-16202.i707_i505


title: SLX-14713.i729_i505


title: SLX-14713.i728_i510


title: SLX-14713.i728_i508


title: SLX-14713.i728_i506


title: SLX-14713.i727_i510


title: SLX-14713.i728_i502


title: SLX-14713.i727_i508


title: SLX-14713.i727_i506


title: SLX-14713.i727_i511


title: SLX-14713.i727_i505


title: SLX-14713.i727_i502


title: SLX-14713.i727_i503


title: SLX-14713.i726_i510


title: SLX-16202.i703_i503


title: SLX-14713.i726_i503


title: SLX-14713.i726_i506


title: SLX-14713.i726_i511


title: SLX-14713.i726_i502


title: SLX-14713.i724_i503


title: SLX-14713.i724_i510


title: SLX-14713.i724_i502


title: SLX-14713.i724_i506


title: SLX-14713.i728_i503


title: SLX-14713.i723_i510


title: SLX-14713.i723_i503


title: SLX-14713.i721_i505


title: SLX-14713.i722_i507


title: SLX-14713.i721_i511


title: SLX-14713.i722_i508


title: SLX-14713.i722_i503


title: SLX-14713.i721_i508


title: SLX-14713.i722_i511


title: SLX-14713.i722_i505


title: SLX-14713.i722_i502


title: SLX-14713.i722_i506


title: SLX-14713.i721_i510


title: SLX-14713.i721_i503


title: SLX-14713.i720_i510


title: SLX-14713.i720_i503


title: SLX-14713.i720_i502


title: SLX-14713.i720_i506


title: SLX-14713.i721_i502


title: SLX-14713.i719_i506


title: SLX-14713.i719_i510


title: SLX-14713.i719_i511


title: SLX-14713.i720_i505


title: SLX-14713.i719_i503


title: SLX-14713.i719_i505


title: SLX-14713.i719_i508


title: SLX-14713.i723_i507


title: SLX-14713.i720_i511


title: SLX-14713.i718_i511


title: SLX-14713.i718_i508


title: SLX-14713.i718_i510


title: SLX-14713.i718_i506


title: SLX-14713.i716_i506


title: SLX-14713.i716_i508


title: SLX-14713.i718_i503


title: SLX-14713.i716_i510


title: SLX-14713.i719_i502


title: SLX-14713.i718_i505


title: SLX-14713.i718_i507


title: SLX-14713.i716_i503


title: SLX-14713.i716_i505


title: SLX-14713.i718_i502


title: SLX-14713.i715_i521


title: SLX-14713.i715_i522


title: SLX-14713.i715_i520


title: SLX-14713.i715_i517


title: SLX-14713.i715_i516


title: SLX-14713.i714_i522


title: SLX-14713.i714_i521


title: SLX-14713.i715_i515


title: SLX-14713.i722_i510


title: SLX-14713.i714_i518


title: SLX-14713.i714_i517


title: SLX-14713.i714_i515


title: SLX-14713.i714_i516


title: SLX-14713.i712_i522


title: SLX-14713.i714_i513


title: SLX-14713.i716_i507


title: SLX-14713.i712_i521


title: SLX-14713.i712_i518


title: SLX-14713.i712_i520


title: SLX-14713.i712_i517


title: SLX-14713.i712_i516


title: SLX-14713.i712_i513


title: SLX-14713.i711_i522


title: SLX-14713.i711_i521


title: SLX-14713.i711_i517


title: SLX-14713.i711_i515


title: SLX-14713.i711_i518


title: SLX-14713.i710_i522


title: SLX-14713.i710_i518


title: SLX-14713.i711_i513


title: SLX-14713.i710_i521


title: SLX-14713.i710_i520


title: SLX-14713.i707_i518


title: CD19negCD22neg non-B cells from FL31


title: SLX-14713.i707_i521


title: SLX-14713.i710_i513


title: SLX-14713.i710_i515


title: SLX-14713.i707_i516


title: SLX-14713.i712_i515


title: SLX-14713.i707_i520


title: SLX-14713.i706_i515


title: SLX-14713.i707_i517


title: SLX-14713.i705_i521


title: SLX-14713.i711_i516


title: SLX-14713.i705_i513


title: SLX-14713.i705_i515


title: SLX-14713.i711_i520


title: SLX-14713.i706_i517


title: SLX-14713.i704_i515


title: SLX-14713.i707_i522


title: SLX-14713.i704_i513


title: SLX-14713.i707_i515


title: SLX-14713.i705_i517


title: SLX-14713.i706_i516


title: SLX-14713.i703_i522


title: SLX-14713.i703_i517


title: SLX-14713.i702_i522


title: SLX-14713.i702_i516


title: SLX-14713.i702_i517


title: SLX-14712.i729_i516

description: SLX-14712.i729_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14713.i701_i522


title: SLX-14713.i703_i516


title: SLX-14713.i703_i515


title: SLX-14713.i706_i513


title: SLX-14713.i701_i515


title: SLX-14712.i728_i522

description: SLX-14712.i728_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i728_i521

description: SLX-14712.i728_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i729_i521

description: SLX-14712.i729_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i729_i515

description: SLX-14712.i729_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i728_i516

description: SLX-14712.i728_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14713.i704_i517


title: SLX-14712.i728_i515

description: SLX-14712.i728_i515.HWFHFBBXX.s_3.r_1.fq.gz