title: LX2 with 50ng/ml rhBMP9,biological rep3

city: Shanghai

first: Peng

last: Li

address: Chongqing nanlu 280

department: Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education

institute: Shanghai JiaoTong University School of Medicine

description: gene expression after treatment with 50ng/ml recombinant human BMP9 proteins fo 24 hours.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Gene Spring Software 14.5 (Agilent technologies, Santa Clara, CA, US).

label: Biotin

source_name: LX2, 50ng/ml rhBMP9, 24h

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: human hepatic stellate cell line LX2 were cultured in DMEM medium supplemented with 10% FBS

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n  AM1556 ) following the manufacturer's instructions.

treatment_protocol: human hepatic stellate cell line LX2  were serum-starved for 12 hours and treated with 0 or 50 ng/ml recombinant human BMP9 proteins for another 24 hours.

value: Hepatic stellate cell line LX2

tag: agent


title: H99-vivo Sample 115

status: Public on Sep 05 2019

type: SRA

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

country: USA

institute: Duke University School of Medicine

library_source: transcriptomic

data_processing:
The quality filtering and adaptor trimming were performed using Cutadapt (v 1.12).
Paired-read alignment for RNA-seq data was carried out against the gene set for C. neoformans var. grubii H99 (CNA3)  excluding non-coding RNAs and mitochondria genes, using STAR (v 2.5.3a).
The expected read count for each gene was computed based on a maximum likelihood estimate, derived from an Expectation Maximization algorithm in RSEM (v1.2.31).
The expected count data were then converted to counts per million (CPM) and normalized by adjusting with the effective library size via the calcNormFactors function implemented in edgeR (v. 3.16.5).
The DEGs were determined by using the negative binomial generalized linear models with quasi-likelihood tests (glmQLFit and glmQLFTest functions in the edgeR package).
Genome_build: CNA3 (GCA_000149245.3)
Supplementary_files_format_and_content: Tab-delimited text files containing expected counts of all genes for all samples.
Supplementary_files_format_and_content: Tab-delimited text files containing FDR P-values of differential gene expression test for each comparison.
Supplementary_files_format_and_content: Tab-delimited text files containing the Log fold-changes of differential gene expression test for each comparison.

molecule: total RNA

organism: Cryptococcus neoformans

source_name: yeast cell

growth_protocol: The strains were extracted from five different culture conditions for 24 hours including growth in yeast extrace-peptone-dextrose (YPD), starvation-low-iron medium (SLIM) and Pigeon Guano (PG) medium, macrophages, and rabbit cerebrospinal fluid

extract_protocol:
These lyophilized samples were treated with Trizol and total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.
Library preparation was prepared by shearing the RNA and adapted for Illumina sequencing using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA).

tag: isolate

tag: strain

value: VNI

tag: source

value: Clinic

tag: condition

value: rabbit cerebrospinal fluid

tag: repeat

value: Rep 1


title: A5-vivo Sample 117

value: Environment


title: LX2 with 50ng/ml rhBMP9,biological rep2

type: RNA

country: China

organism: Homo sapiens

tag: cell line


title: TgSesn2 Immobilized Set1 Rep 3

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

data_processing:
Sequencing reads were pre-processed by means of a pipeline that used FastQC, to asses read quality, and Cutadapt 1.7.1 to trim sequencing reads, eliminating Illumina adaptor remains, and to discard reads that were shorter than 30 bp.
The resulting reads were mapped against the mouse transcriptome (GRCm38, release 76; aug2014 archive) and quantified using RSEM v1.2.20.
Data were normalized using Voom with the Bioconductor package EdgeR-limma
Genome_build: GRCm38, release 76
Supplementary_files_format_and_content: tab-delimited text files include Voom-normalized counts per million reads sequenced

organism: Mus musculus

source_name: Tibialis anterior muscle

extract_protocol:
Tibialis anterior muscleswere removed, flash frozen on dry ice, and RNA was harvested using the combination of QIAzol Lysis Reagent and RNAeasy minikit columns (Qiagen) following the manufacturer’s instructions.
cDNA library preparation and amplification were performed from 200 ng total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina.  RNAseq was performed in two sets. Sets are indicated in the sample and file names (Set1 and Set2).
RNAseq using Illumina Hiseq 2500

tag: tissue

value: Skeletal muscle

tag: age

value: 4 months

tag: genotype

tag: Sex

value: male


title: LX2 with 50ng/ml rhBMP9,biological rep1


title: LX2 with 0ng/ml rhBMP9,biological rep3

description: gene expression after treatment with 0ng/ml recombinant human BMP9 proteins fo 24 hours.

source_name: LX2, 0ng/ml rhBMP9, 24h

value: control


title: PY 302

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to UCSC human genome build GRCh38
Gene counts were obtained using featureCounts on GENCODE V26 annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: genecounts_20190903.txt

source_name: Nasal Polyp Tissue

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted by double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenolchloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA), followed by Qiagen RNeasy Micro clean-up (Qiagen, Hilden, Germany).
cDNA libraries were prepared with 2 ng total RNA input and 1 μl of a 1:50,000 dilution of ERCC RNA Spike-in Controls (Ambion®, Thermo Fisher Scientific, Waltham, MA, USA) using the SMARTSeq v2 protocol with the following modifications: 1) 20 μM template switch oligos, and 2) 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA).
The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on Perkin Elmer Labchip GX system (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed PE sequencing run of 2x151 cycles on Illumina HiSeq 4000 platform (30 samples/lane).

treatment_protocol: Not applicable

value: Nasal Polyp Tissue


title: Tu401-vivo Sample 113

value: VNBI


title: LX2 with 0ng/ml rhBMP9,biological rep2


title: PY 301


title: LX2 with 0ng/ml rhBMP9,biological rep1


title: Chimpanzee Bone WGBS

city: Jerusalem

first: David

last: Gokhman

address: Givat Ram, Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

description:
WGBS
Whole-genome bisulfite sequencing (WGBS) was done on DNA extracted from a chimpanzee skull.

library_source: genomic

data_processing:
Sequence quality was evaluated using FastQC software v0.11.2. TRIMMOMATIC v.0-32 was used to filter low quality bases with the following parameters: -phred33 LEADING:30 TRAILING:30 MAXINFO:70:0.9 MINLEN:70. Paired-end sequencing reads were mapped to bisulfite converted human or chimpanzee (hg19, panTro4) reference genome using Bismark v0.14.3 and bowtie2 v2.2.4 not allowing multiple alignments and using the following parameters: --bowtie2 --non_bs_mm --old_flag -p 4. Potential PCR duplicates were removed using Bismark’s deduplicate_bismark_alignment_output.pl Perl program. Bismark’s bismark_methylation_extractor script was used to produce methylation calls with the following parameters: -p --no_overlap --comprehensive --merge_non_CpG --no_header --bedGraph --multicore 2 --cytosine_report. Examination of the M-bias plots led us to ignore the first 5 bp of both reads in human samples. Custom scripts were used to summarize methylation levels at CpG sites based on the frequencies of methylated and unmethylated mapped reads on both strands.
Genome_build: panTro4 (Pan_troglodytes-2.1.4)
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

organism: Pan troglodytes

source_name: Bone

extract_protocol: DNA was extracted from bones using QIAamp® DNA Investigator kit (56504, Qiagen). Bones were cut to thin slices (0.2-0.5 mm) and then thoroughly washed (X5) with PBS, to clean samples from blood. Bones were crushed with mortar and pestle in liquid nitrogen and 100 mg bone powder was taken to extract DNA according to the protocol "Isolation of Total DNA from Bones and Teeth" of the DNA Investigator kit.

value: Bone


title: PY 256


title: TgSesn2 Immobilized Set1 Rep 4


title: TgSesn2 Immobilized Set1 Rep 1


title: PY 130


title: A1-vivo Sample 112


title: Tu401-MP_2 Sample 109

value: macrophage

value: Rep 2


title: Tu401-MP_1 Sample 108


title: C23-vivo Sample 111


title: TgSesn2 Basal Set1 Rep 4


title: PY 127


title: TgSesn2 Immobilized Set1 Rep 2


title: TgSesn2 Basal Set1 Rep 3


title: TgSesn2 Basal Set1 Rep 2


title: SCT 35

source_name: Nasal Polyp Inferior Turbinate

value: Nasal Polyp Inferior Turbinate


title: Tu401-MP_2 Sample 110


title: TgSesn2 Basal Set1 Rep 1


title: Bt85-MP_2 Sample 105


title: Bt85-MP_2 Sample 106


title: Tu401-MP_1 Sample 107


title: PY 21


title: Bt85-MP_1 Sample 103


title: TgSesn1 Immobilized Set1 Rep 3


title: SCT 33


title: TgSesn1 Immobilized Set1 Rep 2


title: Bt85-MP_1 Sample 104


title: SCT 32


title: HLC_rep2

city: Tokyo

first: Stéphane

last: Poulain

address: Fw-203, 4-6-1, Komaba, Meguro-ku

department: Institute of Industrial Science

country: Japan

institute: The University of Tokyo

data_processing:
Basecalls performed using CASAVA version ???
Demultiplexing, filtering, mapping and molecule assembly were performed with the MOIRAI pipeline OP-WORKFLOW-CAGEscan-short-reads-v2.1 (Hasegawa et al., BMC Bioinformatics, 2014. doi: 10.1186/1471-2105-15-144).
Conversion from single pairs in BAM format to single pairs in BED12 format was done with https://github.com/Population-Transcriptomics/pairedBamToBed12
Assembly of single pairs in BED12 format to single molecules in BED12 format was done with https://github.com/mmendez12/umicount
CAGE peaks were called and gene expression tables generated using the CAGEr package (Haberle et al., Nucleic Acids Research, 2015. doi: 10.1093/nar/gkv054).
Genome_build: hg38
Supplementary_files_format_and_content: BED12 files, one RNA molecule per line; the score indicates how many read pairs were used to assemble the molecule.

source_name: induced Pluripotent Stem Cells

growth_protocol: Human iPSCs were cultured following the protocol described by Si-Tayeb et al., Hepatology, 2010 (doi: 10.1002/hep.23354).

extract_protocol:
Total RNA was harvested using Trizol reagent. 250ng of total RNA from each sample were used for the construction of the sequencing libraries.
NanoCAGE sequencing libraries were prepared according to the protocol described by Poulain et al., Methods in Molecular  Biology, 2017 (doi: 10.1007/978-1-4939-6716-2_4).

value: induced Pluripotent Stem Cells

tag: cell culture step

tag: cell differentation stage

value: Heptocytes-Like Cells (HLC)

tag: nanocage template-switching oligo barcode sequence

value: TCGAGC

tag: nanocage template-switching oligo barcode number


title: HE_rep3

value: Hepatic Endoderm (HE)

value: GAGTGA


title: SCT 31


title: HLC_rep1

value: GTATAC


title: HLC_rep3

value: ACATGA


title: SCT 34


title: Sesn1 KO Basal Set2 Rep 2

value: Skeletal muscle


title: HE_rep1

value: CACTGA


title: SCT 30


title: DE_rep3

value: Definitive Endoderm (DE)

value: GTATGA


title: DE_rep2

value: GCTCTC


title: TgSesn1 Basal Set1 Rep 3

value: 4 months

value: male


title: SCT 29


title: SCT 28


title: CHC193-MP_2 Sample 102

value: VNI

value: Clinic

value: macrophage


title: H99-MP_1 Sample 98

value: Rep 1


title: TgSesn1 Basal Set1 Rep 1


title: H99-MP_2 Sample 100

value: Rep 2


title: CHC193-MP_2 Sample 101


title: H99-MP_2 Sample 99


title: DE_rep1

value: induced Pluripotent Stem Cells

value: GAGATA


title: HE_rep2

value: Hepatic Endoderm (HE)

value: CTGACG


title: SCT 23

value: Nasal Polyp Inferior Turbinate


title: iPSC_CONTROL_rep3

value: CACGAT


title: TgSesn1 Immobilized Set1 Rep 1

value: Skeletal muscle


title: A5-MP_2 Sample 96

value: Environment


title: TgSesn1 Basal Set1 Rep 4


title: A5-MP_2 Sample 95


title: SCT 22


title: iPSC_CONTROL_rep2

value: ATCGTG


title: 4C for Snx2 locus in wt mESC, biological replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Library strategy: 4C
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on multiple independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
ChIPseq: Sequenced reads were aligned using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within ).
Hi-C: Raw reads were filtered and aligned using HiC-Pro 2.9.0 (Servant et al., 2015). Further analysis was performed using the R package GENOVA.
4C: Raw reads were mapped using the 4C-mapping pipeline from the de Wit lab (https://github.com/deWitLab/4C_mapping). Mapped reads were further processed using peak_C from the de Wit lab (https://github.com/deWitLab/peakC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools). Bed files containing peak positions were generated from the .narrowPeak output file from MACS2. HiC allValidPairs files were generated by HiC-Pro 2.9.0. 4C wig files for replicates were generated from the filtered_reads output from peak_C by adding a wiggle file header.

source_name: embryonic stem (ES) cells

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
4C was performed on 10^7 mES cells, crosslinked in 2% para-formaldehyde, digested with DpnII and Csp6l. For details see Kaaji et al, 2019.
4C libraries were generated according to van de Werken et al, 2012. For details, see Kaaji et al, 2019.

tag: cell type

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

value: wt


title: SCT 21


title: TgSesn1 Basal Set1 Rep 2

value: 4 months

value: male


title: A5-MP_1 Sample 94

value: VNI

value: macrophage


title: H99-MP_1 Sample 97

value: Clinic

value: Rep 1


title: A5-MP_1 Sample 93


title: SCT 20


title: iPSC_CONTROL_rep1

value: induced Pluripotent Stem Cells

value: ACAGAT


title: SCT 19


title: 4C for Snx2 locus in AdnpKO mESC, biological replicate 2

value: Adnp KO


title: A1-MP_2 Sample 92

value: Rep 2


title: 4C for Snx2 locus in AdnpKO mESC, biological replicate 1


title: A1-MP_2 Sample 91


title: SCT 18

value: Nasal Polyp Inferior Turbinate


title: ChIPseq for biotin in untagged parental cell line

data_processing:
Samples were pooled and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument. Some samples were sequenced on multiple independent lanes and raw fastq files need to be pooled prior to mapping. These are indicated with "a" and "b" in the file name.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
ChIPseq: Sequenced reads were aligned using STAR 2.5.0a (--alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within ).
Hi-C: Raw reads were filtered and aligned using HiC-Pro 2.9.0 (Servant et al., 2015). Further analysis was performed using the R package GENOVA.
4C: Raw reads were mapped using the 4C-mapping pipeline from the de Wit lab (https://github.com/deWitLab/4C_mapping). Mapped reads were further processed using peak_C from the de Wit lab (https://github.com/deWitLab/peakC).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools). Bed files containing peak positions were generated from the .narrowPeak output file from MACS2. HiC allValidPairs files were generated by HiC-Pro 2.9.0. 4C wig files for replicates were generated from the filtered_reads output from peak_C by adding a wiggle file header.

extract_protocol:
10^7 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Kaaij et al, 2019.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.

tag: antibody

value: Strepdavidin Dynabeads M280 (Thermofisher)


title: SCP 212


title: S2KO_EB_D4-2

city: New York City

first: Lin

last: Tian

state: New York

address: Mortimer B. Zuckerman Research Center, 417 East 68th Street

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
QC: FastQC v0.11.5
Alignement: Bowtie2 for ChIPseq, STAR/RSEM for RNAseq
ChIPseq sorting, normalization, and visualization: Sam Tools & HOMER
Genome_build: mm10
Supplementary_files_format_and_content: ChIPSeq: genome browser tracks in .tdf
Supplementary_files_format_and_content: RNASeq: Normalized Counts in .txt

source_name: Embryoid body

growth_protocol: For ChIPseq, pluripotent mouse embrynoic stem cell (mESC) E14 were suspended in LIF free media to differentiate to embryonic bodies(EBs) for 3days, and then treated with either SB431542 or Activin for 2hours. These EBs and pluripotent ESCs were collected for ChIPseq using Smad2, Smad3, Smad4 and Foxh1 antibodies. For RNAseq, wild type E14 at pluripotent stage (D0)  and EBs at Day 4 (D4) from wild type E14, Smad2KO (S2KO), Smad3KO (S3KO), Smad2/3DKO (S2/3DKO) were used.

extract_protocol: For ChIPseq, Lysates were clarified from sonicated cells and transcription factor-DNA complexes were isolated with antibody. For RNAseq, PrepEase RNA Spin Kit (Affymetrix) were used for RNA extraction.


title: SCP 213


title: 4C for Hsf2bp locus in wt mESC, biological replicate 1


title: S2/3DKO_EB_D4-1


title: S3KO_EB_D4-2


title: S2KO_EB_D4-1


title: 4C for Hsf2bp locus in AdnpKO mESC, biological replicate 2


title: S2/3DKO_EB_D4-2


title: 4C for Hsf2bp locus in wt mESC, biological replicate 2


title: A1-MP_1 Sample 89

tag: isolate

value: Environment


title: 4C for Hsf2bp locus in AdnpKO mESC, biological replicate 1


title: 4C for Snx2 locus in wt mESC, biological replicate 1


title: A1-MP_1 Sample 90

tag: strain


title: SCP 210


title: SCP 209


title: C23-MP_2 Sample 88

tag: source


title: C23-MP_2 Sample 87

tag: condition


title: S3KO_EB_D4-1


title: C23-MP_1 Sample 86

tag: repeat


title: 4C for Cohesin V1 locus in wt mESC, biological replicate 2


title: C23-MP_1 Sample 85


title: EB_D4-2

tag: cell line

value: Wild type


title: 4C for Cohesin V1 locus in wt mESC, biological replicate 1

value: embryonic stem (ES) cells


title: SCP 206

tag: tissue


title: SCP 204


title: 4C for Cohesin V1 locus in AdnpKO mESC, biological replicate 2

value: hybrid 129-C57BL/6


title: C23-LIM_2 Sample 84

value: starvation-low-iron media


title: SCP 203


title: EB_D4-1


title: ES_D0-2

source_name: Embryonic stem cell


title: C23-LIM_2 Sample 83


title: SCP 202


title: 4C for Cohesin V1 locus in AdnpKO mESC, biological replicate 1


title: C23-LIM_1 Sample 82


title: ES_D0-1


title: C23-PG_2 Sample 80

value: pigeon guano


title: SCP 201


title: 4C for Cohesin V2 locus in wt mESC, biological replicate 2

value: wt


title: C23-LIM_1 Sample 81

value: VNI


title: TT 33

value: Nasal Polyp Tissue


title: TT 35


title: 4C for Cohesin V2 locus in wt mESC, biological replicate 1


title: 4C for Cohesin V2 locus in AdnpKO mESC, biological replicate 2


title: 4C for Cohesin V2 locus in AdnpKO mESC, biological replicate 1


title: EB-SB_Foxh1_ChIPseq

tag: chip antibody

value: Foxh1 (Abcam, 49133)


title: EB-SB_Smad4_ChIPseq

value: Smad4 (Santa Cruz, 7966X and Abcam, 40759)


title: TT 32


title: TT 31


title: EB-AC_Smad3_ChIPseq

value: Smad3 (Cell Signaling Technology, 9523S)


title: 4C for chr7 viewpoint v4 in wt mESC, biological replicate 2

tag: genotype


title: C23-PG_2 Sample 79

value: Clinic


title: C23-PG_1 Sample 78

value: Rep 1


title: EB-AC_Foxh1_ChIPseq


title: EB-SB_Smad3_ChIPseq


title: TT 30


title: TT 29


title: 4C for chr7 viewpoint v4 in AdnpKO mESC, biological replicate 1

value: Adnp KO


title: C23-YPD_2 Sample 76

value: yeast extract-peptone-dextrose

value: Rep 2


title: EB-AC_Smad4_ChIPseq


title: C23-YPD_2 Sample 75


title: 4C for chr7 viewpoint v4 in wt mESC, biological replicate 1


title: 4C for chr7 viewpoint v2 in AdnpKO mESC, biological replicate 2


title: EB-SB_Smad2_ChIPseq

value: Smad2 (Cell Signaling Technology, 5339S)


title: TT 22


title: TT 23


title: 4C for chr7 viewpoint v4 in AdnpKO mESC, biological replicate 2


title: 4C for chr7 viewpoint v2 in AdnpKO mESC, biological replicate 1


title: ES_Foxh1_ChIPseq


title: EB_AC_Input


title: C23-YPD_1 Sample 74


title: C23-PG_1 Sample 77


title: 4C for chr7 viewpoint v2 in wt mESC, biological replicate 1


title: ES_Smad4_ChIPseq


title: ES_Smad3_ChIPseq


title: Tu401-LIM_2 Sample 72

value: VNBI

value: Environment


title: TT 19


title: TT 28


title: ES_Smad2_ChIPseq


title: 4C for chr7 viewpoint v1 in wt mESC, biological replicate 2

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/6


title: 4C for chr7 viewpoint v1 in AdnpKO mESC, biological replicate 1


title: TT 18


title: C23-YPD_1 Sample 73


title: Tu401-LIM_1 Sample 69

value: starvation-low-iron media


title: TT 20


title: 4C for chr7 viewpoint v1 in AdnpKO mESC, biological replicate 2


title: ES_Input


title: Tu401-LIM_2 Sample 71


title: DCCmutant_RNA-seq

city: San Francisco

first: Elphege

middle: P

last: Nora

state: CA

address: 555 Mission Bay Blvd S

department: CVRI

institute: UCSF

description:
BMEA021C and BMEA033C replicates used mixed-stage embryos. BMEA033F used a population skewed towards older embryos.
WT_8rexDeletion_DCCmutant_RNAseq.txt

data_processing:
Libraries were sequenced with 50 bp reads on an Illumina HiSeq4000 platform. Reads were processed by trimming adapters using cutadapt version 1.2.1, aligning to the ce11 reference genome using TopHat version 2.1.1, and assembling using Cufflinks version 2.2.1.
All replicates were combined using Cuffmerge.
Expression levels (fpkm) and fold changes were analyzed using cummeRbund version 2.20.0.
Genome_build: ce11
Supplementary_files_format_and_content: The processed file, derived from cufflinks output, is a tab-delimited table including expression levels (FPKM) for each transcript identified by cufflinks in embryos of the three genotypes as well as log2 fold changes, p values, and q values for 8rexΔ and DCC mutant compared to wild-type embryos.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: embryos

growth_protocol: Worms were grown on RNAi plates with HT115 bacteria with either sdc-2 RNAi (for DCC mutant) or pL4440 empty vector (for wild type and 8rexΔ).

extract_protocol:
RNA was extracted using TRIzol as in Brejc et al 2017.
PolyA RNA was purified and fragmented, cDNA was synthesized, and NEXTflex DNA adaptors were ligated as in Brejc et al 2017.

treatment_protocol: For some replicates, mixed-stage embryos (majority pre-comma stage) were isolated by bleaching gravid hermaphrodites. Other replicates were skewed towards older embryos by bleaching young adults (68-70 hr after plating L1s) to isolate young embryos, letting the embryos develop at 20° C for 7-8 hr until the majority were at the three-fold stage, and then freezing in M9 buffer.

tag: strain name

value: TY0810 grown on sdc-2 RNAi bacteria

value: sdc-2(y93, RNAi)


title: PY 211

value: Nasal Polyp Tissue


title: 8rexDeletion_RNA-seq

description:
BMEA021B and BMEA033B replicates used mixed-stage embryos. BMEA033E, BMEA036C, and BMEA036F replicates used populations skewed towards older embryos.
WT_8rexDeletion_DCCmutant_RNAseq.txt


title: 4C for chr7 viewpoint v3 in AdnpKO mESC, biological replicate 2


title: TT 21


title: PY 210


title: Tu401-PG_2 Sample 68

value: pigeon guano


title: Tu401-PG_2 Sample 67


title: WT_RNA-seq

description:
BMEA021A and BMEA033A replicates used mixed-stage embryos. BMEA033D, BMEA036A, and BMEA036D replicates used populations skewed towards older embryos.
WT_8rexDeletion_DCCmutant_RNAseq.txt

value: wild type


title: Tu401-PG_1 Sample 66


title: PY 212


title: 4C for chr7 viewpoint v3 in AdnpKO mESC, biological replicate 1


title: PY 209


title: Tu401-YPD_2 Sample 64


title: rex-14rex-47rex-8insertion_IgG_ChIP-seq

data_processing:
Adapters were trimmed using cutadapt version 1.2.1 (Martin, 2011), and reads were then aligned to the ce11 genome using bowtie2 version 2.3.0 (Langmead and Salzberg, 2012) with default settings. For comparisons involving strains with rex site insertions, the reference genome was modified to incorporate the rex insertions.
Reads were sorted using SAMtools version 1.3.1 (Li et al., 2009) and read coverage in bigwig files was calculated by normalizing the read number in each 50 bp bin to the total read number using the bamCoverage function in deepTools version 2.5.0.1 (Ramírez et al., 2016) with the “normalizeUsingRPKM” option. Analysis of data from wild-type and 8rexΔ strains was performed with two combined biological replicates, and one replicate was used for data from TY5872 8rexΔ plus rex-32 & rex-8 and TY5867 3rexΔ plus rex-14, rex-8 & rex-47 strains.
Genome_build: ce11
Supplementary_files_format_and_content: bigWig files contain reads normalized by the total read number (RPKM) in 50 bp bins

source_name: mixed-stage embryos

growth_protocol: Worms were grown on RNAi plates with HT115 bacteria carrying the empty plasmid vector pL4440. Mixed stage embryos were isolated by bleaching and frozen in liquid nitrogen.

extract_protocol:
Embryos were ground with 50 strokes in a 2 mL dounce homogenizer. Sarkosyl was added to a final concentration of 0.1% and chromatin was sheared in an S2 Covaris with duty cycle 20%, intensity 8, and 200 cycles/burst for 30 cycles of 60 sec with 45 sec of rest for a total time of 52 min. The extract was centrifuged at maximum speed for 15 min at 4° C. Supernatant containing approximately 2 mg total protein was incubated with 6.6 μg rabbit polyclonal anti-DPY-27 (rb699) (Chuang et al., 1994), rat polyclonal anti-SDC-3 (PEM4A) (Crane et al., 2015), or random IgG antibodies overnight at 4° C in a volume of at least 500 μl. 50 μl of Protein A Dynabeads (ThermoFisher Scientific, 10002D) were washed in FA buffer three times, added to the immunoprecipitation, and mixed at 4° C for at least 2 hr. Beads were then washed and DNA eluted as in (Kruesi et al., 2013).
We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Kruesi et al 2013.

treatment_protocol: Embryos were washed once in 2% formaldehyde in M9 buffer and then fixed for 30 min with gentle rocking in 50 mL 2% formaldehyde in M9 buffer. Embryos were washed in 10mM Tris-HCl (pH 7.5) and then in FA buffer (150 mM NaCl, 50 mM HEPES-KOH pH 7.6, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) and resuspended in FA buffer with protease inhibitors (5 mM DTT, protease inhibitor cocktail, 1 mM PMSF) to a total volume of 1 mL.

value: IgG


title: PY 208


title: 4C for chr7 viewpoint v1 in wt mESC, biological replicate 1

value: wt


title: 4C for chr7 viewpoint v3 in wt mESC, biological replicate 1


title: Tu401-YPD_2 Sample 63


title: PY 207


title: PY 206


title: Tu401-YPD_1 Sample 62

value: Rep 1


title: 8rexDeletionPlusrex-32rex-8_IgG_ChIP-seq


title: 4C for chr7 viewpoint v3 in wt mESC, biological replicate 2


title: 4C for Cdx2 locus in AdnpKO mESC, biological replicate 2

value: Adnp KO


title: PY 204


title: Bt85-LIM_2 Sample 60

value: Clinic


title: rex-14rex-47rex-8insertion_SDC-3_ChIP-seq


title: Tu401-PG_1 Sample 65


title: PY 205


title: 4C for Cdx2 locus in wt mESC, biological replicate 1


title: EB-AC_Smad2_ChIPseq


title: 4C for Cdx2 locus in wt mESC, biological replicate 2


title: 8rexDeletionPlusrex-32rex-8_DPY-27_ChIP-seq


title: 8rexDeletionPlusrex-32rex-8_SDC-3_ChIP-seq


title: Tu401-LIM_1 Sample 70


title: Tu401-YPD_1 Sample 61

value: yeast extract-peptone-dextrose


title: 4C for Cdx2 locus in AdnpKO mESC, biological replicate 1


title: PY 203


title: 8rexDeletion_SDC-3_ChIP-seq


title: 4C for Arl4c locus in wt mESC, biological replicate 2


title: 8rexDeletion_DPY-27_ChIP-seq


title: 4C for Arl4c locus in wt mESC, biological replicate 1


title: PY 157


title: PY 202


title: WT_IgG_ChIP-seq


title: Bt85-LIM_1 Sample 58


title: CC 209

source_name: Control Inferior Turbinate

value: Control Inferior Turbinate


title: CC 210


title: WT_SDC-3_ChIP-seq


title: 8rexDeletion_IgG_ChIP-seq


title: CC 208


title: 4C for Arl4c locus in AdnpKO mESC, biological replicate 1


title: WT_DPY-27_ChIP-seq


title: rex-14rex-47rex-8insertion_Hi-C

data_processing:
Libraries were sequenced with Illumina's HiSeq 4000 Platform using 100 bp paired end reads. Reads were mapped to the ce11 reference genome, binned at 50 kb, and iteratively corrected using scripts derived from those available at https://bitbucket.org/mirnylab/hiclib as in Brejc et al 2017. For genotypes with two replicates, interaction frequencies after iterative correction from the two replicates were combined.
To quantify TAD boundaries, we calculated insulation scores from the Hi-C interaction data as in Crane et al 2015 using the following parameters: insulation square 500000, insulation delta span 200000, insulation mode mean, and noise threshold 0.1.
To correct for experimental variation in the decay of chromatin contacts with genomic distance, we calculated Hi-C Z scores using a LOESS method (Imakaev et al 2012) with scripts available at https://github.com/dekkerlab/cworld-dekker
Genome_build: ce11
Supplementary_files_format_and_content: .matrix files are tab-delimited tables of genome-wide interaction frequencies iteratively corrected and normalized for read depth as in Crane et al 2015.
Supplementary_files_format_and_content: .zScore.matrix files are tab-delimited tables of Z scores.
Supplementary_files_format_and_content: .insulation files give the insulation score and delta vector for each 50 kb bin in the genome, as defined in Crane et al 2015

source_name: mixed stage embryos

growth_protocol: Wild-type and rex site deletion and insertion worms were grown on NGM plates with HB101 bacteria, and sdc-2(y93) worms were grown on RNAi plates with HT115 bacteria carrying an sdc-2 (RNAi) plasmid. Mixed stage embryos were isolated by bleaching.

extract_protocol:
We purfied, sheared, and size-selected DNA and pulled down biotinylated fragments as in Brejc et al 2017.
We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Brejc at al 2017.

treatment_protocol: We isolated nuclei, digested with DpnII restriction enzyme, filled in the restriction overhangs with biotinylated nucleotides, and ligated as in Brejc et al 2017.


title: Bt85-LIM_2 Sample 59

value: VNBI

value: Rep 2


title: Bt85-PG_1 Sample 53


title: CC 207


title: Bt85-LIM_1 Sample 57


title: rex-47rex-8insertion_Hi-C


title: Bt85-YPD_2 Sample 52


title: 4C for Arl4c locus in AdnpKO mESC, biological replicate 2

value: embryonic stem (ES) cells


title: Bt85-PG_1 Sample 54


title: 4C for Abcc5 locus in wt mESC, biological replicate 1

value: hybrid 129-C57BL/6


title: Bt85-PG_2 Sample 56


title: Bt85-PG_2 Sample 55


title: CC 206


title: 4C for Abcc5 locus in wt mESC, biological replicate 2


title: 4C for Abcc5 locus in AdnpKO mESC, biological replicate 1


title: Bt85-YPD_2 Sample 51


title: rex-32insertion_Hi-C


title: Input of ChIPseq for H3K27ac in AdnpKO mES cells, replicate 2

value: anti H3K27ac (Abcam, ab2749)


title: Bt85-YPD_1 Sample 49


title: SCP 156

value: Nasal Polyp Inferior Turbinate


title: SCP 157


title: 8rexDeletionPlusrex-32rex-8_Hi-C


title: SCP 155


title: CHC193-LIM_2 Sample 47

value: VNI

value: starvation-low-iron media


title: DCCmutant_Hi-C

value: TY0810 grown on sdc-2 RNAi bacteria

value: sdc-2(y93, RNAi)


title: 4C for Abcc5 locus in AdnpKO mESC, biological replicate 2


title: Input of ChIPseq for H3K27ac in AdnpKO mES cells, replicate 1


title: SCP 154


title: CHC193-LIM_2 Sample 48


title: 8rexDeletionPlusrex-32_Hi-C


title: SCP 182


title: rex-47insertion_Hi-C


title: 8rexDeletion_Hi-C


title: SCP 75


title: Input of ChIPseq for H3K27ac in wt mES cells, replicate 2


title: ChIPseq for H3K27ac in AdnpKO mES cells, replicate 2


title: SCP 404


title: ChIPseq for H3K27ac in AdnpKO mES cells, replicate 1


title: ChIPseq for H3K27ac in wt mES cells, replicate 2


title: CHC193-LIM_1 Sample 46


title: 6rexDeletion_Hi-C


title: CHC193-LIM_1 Sample 45


title: Bt85-YPD_1 Sample 50


title: 3rexDeletion_Hi-C


title: Input of ChIPseq for H3K27ac in wt mES cells, replicate 1


title: CHC193-PG_2 Sample 44

value: pigeon guano


title: ChIPseq for H3K27ac in wt mES cells, replicate 1

value: wt


title: SCP 14


title: CHC193-PG_2 Sample 43


title: rex-47Deletion_Hi-C


title: SCP 10


title: WT_Hi-C

value: wild type


title: SCP 1


title: PY 156

value: Nasal Polyp Tissue


title: CHC193-YPD_2 Sample 40

value: Clinic


title: ChIPseq for Rad21 in AdnpKO mES cells, replicate 2

value: Adnp KO

value: anti Rad21 (Abcam, ab992)


title: CHC193-PG_1 Sample 42

value: Rep 1


title: CHC193-PG_1 Sample 41


title: CHC193-YPD_2 Sample 39

value: yeast extract-peptone-dextrose

value: Rep 2


title: Input of ChIPseq for Rad21 in AdnpKO mES cells, replicate 2

value: embryonic stem (ES) cells

value: hybrid 129-C57BL/6


title: PY 154


title: PY 155


title: ChIPseq for Rad21 in AdnpKO mES cells, replicate 1


title: CHC193-YPD_1 Sample 38


title: PY 404


title: Input of ChIPseq for Rad21 in wt mES cells, replicate 2


title: Input of ChIPseq for Rad21 in AdnpKO mES cells, replicate 1


title: ChIPseq for Rad21 in wt mES cells, replicate 2


title: CHC193-YPD_1 Sample 37


title: Input of ChIPseq for Rad21 in wt mES cells, replicate 1


title: H99-LIM_2 Sample 36


title: PY 75


title: PY 182


title: ChIPseq for Rad21 in wt mES cells, replicate 1


title: PY 18


title: H99-LIM_1 Sample 34


title: H99-LIM_2 Sample 35


title: Lidocaine_1

city: Xi'an

first: Hailiang

last: Du

state: Shaanxi

address: 277 West Yanta Road

department: Anesthesiology

institute: The First Affiliated Hospital of Xi'an Jiaotong University

description: Gene expression data from spinal cord tissue of rat in lidocaine group

hyb_protocol: Following labeling, cDNA was hybridized on  gene chip Affymetrix Clariom D rat array .

scan_protocol: GeneChips were scanned scanned with the Affymetrix GeneChip Operating Software (GCOS) installed in a GeneChip Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label: biotin

organism: Rattus norvegicus

source_name: Spinal cord tissue in lidocaine group

label_protocol: Biotinylated cDNA was prepared from 150 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

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

treatment_protocol: The Sprague–Dawley rats were fed at room temperature (25 ± 1℃), the relative humidity was 40%–60%, and the light–dark cycle was 12 h. The animals were kept individually, and the standard rat feed and water were taken at will.The control group was blank control group: no treatment was given. 10% lidocaine (20 μL, L5647-15G, Sigma, MO, USA),  was injected into the intrathecal space of each rat in the lidocaine group. Neurobehavioral tests were performed on rats in each group before injection and 1, 2, 3, and 4 days after the intrathecal injection. On the fourth day, after completing neurobehavioral tests, the spinal cords of all rats from L2 to L6 were removed and immediately stored in liquid nitrogen.

value: Sprague-Dawley

value: Lumbar segment of spinal cord


title: PY 10


title: PY 14


title: Input of ChIPseq for Ctcf in AdnpKO mES cells, replicate 2

value: anti Ctcf (Cell Signaling, #2899)


title: Control_2

description: Gene expression data from spinal cord tissue of rat in control group

source_name: Spinal cord tissue in control group


title: Lidocaine_2


title: Control_3


title: Lidocaine_3


title: Input of ChIPseq for Ctcf in AdnpKO mES cells, replicate 1


title: ChIPseq for Ctcf in AdnpKO mES cells, replicate 2


title: H99-LIM_1 Sample 33

value: VNI

value: starvation-low-iron media


title: #6 10 uM 3

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

institute: DUKE-NUS Graduate Medical School

description: Gene expression data from PC12 cells under various treatment conditions

hyb_protocol: Following fragmentation, samples were hybridized on the Affymetrix Rat RTA-1_0 Transcriptome Array for 16hrs at 45oC.

scan_protocol: GeneChips were washed and stained using the GeneChip® Fluidics Station 450 (Affymetrix). Scanning was done using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed in Affymetrix Expression Console via the RMA method

source_name: PC12 cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 250ng of total RNA (GeneChip® WT PLUS Reagent Kit User Manual, Affymetrix).

growth_protocol: PC12 cells displaying inducible expression of GFP-tagged Huntingtin (exon-1 fragment) with 74Q were seeded at (4 X 105) in gorwth medium.

extract_protocol: total RNA was extracted according to the manufacturer's instructions (Rneasy Mini kit, Qiagen)

treatment_protocol: non-induced (control) or induced (with 1μg/ml doxycycline) cells were treated with Vehicle DMSO. Induced PC12 cells werr then treated with Compound 6 or Compound 3 at 10 uM for 48 hours

tag: treatment


title: H99-PG_2 Sample 32

source_name: yeast cell

value: pigeon guano


title: Control_1


title: PY 1


title: 4C for chr7 viewpoint v2 in wt mESC, biological replicate 2

value: wt


title: ChIPseq for Ctcf in AdnpKO mES cells, replicate 1


title: H99-PG_2 Sample 31


title: H99-PG_1 Sample 30


title: Lung Biopsy, PF, TILD001

city: Phoenix

last: Banovich

state: AZ

address: 445 N. Fifth Street

department: Integrated Cancer genomics division

institute: Translational Genomics Research Institute

data_processing:
Indivual sample reads were input into Cellranger 3.0.2 using reference hg38
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger output format with all samples aggregated together, includes celltype metadata

source_name: Lung Biopsy

extract_protocol:
Custom tissue dissociation
10X 5' Gene Expression (GEX) Library Construction

tag: disease state

value: pulmonary fibrosis (PF)

value: Lung Biopsy


title: Lung Biopsy, control, VUHD69

value: control


title: Input of ChIPseq for Ctcf in wt mES cells, replicate 2


title: H99-PG_1 Sample 29

value: Clinic


title: H99-YPD_2 Sample 28


title: #6 10 uM 2


title: #6 10 uM 1


title: ChIPseq for Ctcf in wt mES cells, replicate 1


title: Input of ChIPseq for Ctcf in wt mES cells, replicate 1


title: 1KD_CIS

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were processed with RNA-seq workflow in CLC Genomics Workbench version 11. Reads were mapped to human reference genome GRCh38 with default setting.
Gene expression is estimated with the EM estimation algorithm and reported as TPM (Transcripts Per Million)
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files with gene expression data in TPM and RPKM

source_name: xenograft ovarian tumor from mouse

extract_protocol:
Total RNA were extracted from A2780 xenograft mouse tumors  that have been stored in RNAlater solution using Qiagen RNeasy Mini Kit.
Sequencing libraries were prepared using KAPA Stranded mRNA seq Kit and run in a single lane using Illumina HiSeq 4000 instrument.

tag: transfection

value: shRNA targeting GDF15

tag: host strain

value: Swiss nude mouse

tag: age (weeks)

value: 8-10 weeks

value: mouse treated with cisplatin


title: #3 10 uM 2


title: #3 10 uM 3


title: H99-YPD_2 Sample 27

value: yeast extract-peptone-dextrose

value: Rep 2


title: #3 10 uM 1


title: 2KD_PBS

value: mouse treated with PBS


title: H99-YPD_1 Sample 26

value: Rep 1


title: NSC-P5-H9-2

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: WT

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human reference genome using hisat2 software.
Reads were counted by HTseq-count.
Differentially expressed genes were calculated by Stringtie.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is table seprated file. And, the content is HTseq counted reads count.

source_name: human neural stem cells

growth_protocol: hMSCs were maintained on gelatin (Sigma)-coated plates (Corning) in -MEM medium (Gibco) containing 10% fetal bovine serum (FBS, Gibco), 0.1 mM non-essential amino acids (Gibco), 1% penicillin/streptomycin (Gibco), and 1 ng/mL FGF2 (JPC). hNSCs were cultured in neural stem cell maintenance medium supplemented with 50% Neurobasal (Gibco), 50% Advanced DMEM/F12 (Gibco), 2 mM GlutaMax, 1×B27 (Gibco), 1×N2 (Gibco), 10 ng/mL human leukemia inhibitory factor (hLIF, Millipore), 2 M SB431542 (Selleck) and 3 M CHIR99021 (Selleck).hNSCs were passaged on Matrigel-coated pltes in neural stem cell maintenance medium (NSMM) containing 50% Neurobasal, 50% Advanced DMEM/F12, 1×B27, 1×N2, 2 mM GlutaMAX, 10 ng/mL hLIF, 2 M SB431542 and 3 M CHIR99021.

extract_protocol:
Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) from 1x106 cells per duplicate and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell type

value: ES-derived  human neural stem cells

value: WT

tag: passage


title: 1KD_PBS


title: NSC-P5-H9-1

description: WT


title: Induced-DMSO 3


title: H99-YPD_1 Sample 25

tag: isolate

value: VNI


title: Lung Biopsy, PF, TILD019


title: 2NT_CIS

value: non-target shRNA


title: NSC-P5-DJ-7-1


title: 2KD_CIS


title: A5-LIM_2 Sample 24

tag: strain

value: Environment

value: starvation-low-iron media


title: ChIPseq for Ctcf in wt mES cells, replicate 2

value: embryonic stem (ES) cells

tag: genetic background

value: hybrid 129-C57BL/6

value: wt

tag: antibody

value: anti Ctcf (Cell Signaling, #2899)


title: NSC-P5-DJ-7-2


title: A5-LIM_2 Sample 23

tag: source

tag: condition

tag: repeat


title: Induced-DMSO 2

tag: cell line


title: 1NT_CIS

value: Swiss nude mouse


title: 2NT_PBS

value: 8-10 weeks


title: Induced-DMSO 1


title: Non-Induced DMSO 3

value: Non-induced


title: MSC-P3-H9-2

description: WT

source_name: human mesenchymal stem cells

value: ES-derived  human mesenchymal stem cells

tag: genotype


title: 1NT_PBS


title: A5-LIM_1 Sample 22


title: Non-Induced DMSO 2


title: Non-Induced DMSO 1


title: Lung Biopsy, PF, TILD030

value: pulmonary fibrosis (PF)

tag: tissue

value: Lung Biopsy


title: A5-LIM_1 Sample 21

value: Rep 1


title: MSC-P3-DJ-7-2


title: A5-PG_2 Sample 20

value: pigeon guano

value: Rep 2


title: Lung Biopsy, PF, TILD006


title: A5-PG_2 Sample 19

value: VNI


title: MSC-P3-DJ-7-1


title: Lung Biopsy, control, THD0005

value: control


title: A5-PG_1 Sample 18

value: Environment


title: siC-Pol2_S5P

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: Pol II CTD (Ser5) ChIP-seq

data_processing:
Reads from ChIP-seq libraries were send to trim-galore to remove adapter contamination and low-quality sequences,
Trimmed sequences were mapped with Bowtie (v2.2.6) using default parameters
Duplicate reads were removed by samtools rmdup -s.
Unique and monoclonal mapped reads were extended to 150 bp based on the average sonicated chromatin DNA length.
Spike-in reads were mapped to drosophila genome(dm6) using same parameters.
Peaks were called using MACS2 with broad peak mode and default settings(qvalue=0.01).
genomeCoverageBed(bedtools) was used to transfer bed files to bedGraph files, then spikein read numbers were used as a normalization factor that equalizes the signal across samples.
genome build: GRCH37/hg19
processed data files format and content: BigWig files of Pol ll, Pol ll S2P and Pol ll S5P ChIP-seq tag density

growth_protocol: Embryonic kidney cell line HEK293T (CRL-11268) were obtained from American Type Culture Collection (ATCC) and were cultured under standard conditions

extract_protocol:
KAPA Hyper Prep Kit (KK8502, KapaBiosystems)
For chromatin PAR-CLIP, chromatin extraction was performed based on a published protocol (Brugiolo et. al., Nucleic Acids Research, 2017, 45(18):10452–65). The chromatin pellet from 3* 15 cm of HEK293T cells was solublized 900 µL chromatin extraction buffer (20 mM Tris-Cl [pH 7.5], 100 mM KCl, 2 mM MgCl2, 2.5 mM CaCl2, 0.3 M sucrose, and 0.1% v/v Triton X-100, 1% protease and phosphatase inhibitor) with 5 U/mL Micrococcal Nuclease (N3755, Sigma) by shaking at 4 ºC for 2 hours. The immunoprecipitation was performed with 5 ug of rabbit anti-hnRNPG antibody (Ab190352, abcam) overnight and 100 uL Protein A beads (10002D, Thermo) for another 4 hours at 4ºC. Co-immunoprecipitated RNA fragments were then washed, end-repaired on-beads, size-selected by SDS-PAGE, and released by Protease K digestion. RNA was purified by Acid-Phenol:Chloroform extraction and overnight ethanol precipitation. For ChIP-seq, we followed the protocol of ChIP-IT® Express kit (53008, Active motif) with Spike-in normalization strategy. The chromatin samples were sheared by sonication into 200-500 bp in size. For each immunoprecipitation reaction, 20 ug of the sample chromatin, 5 ug of the antibody, 10 ng of Spike-in chromatin (53083, Active motif), and 1 ug of Spike-in antibody (61686, Active Motif) were used. After washing, reverse crosslinking, and treatment with RNase A and Protease K, the DNA was purifed by with DNA Clean & Concentrator-5 (D4013, Zymo research).

treatment_protocol: Transfection with 20 nM control siRNA for 48 hours and crosslinked with 1% formaldehyde

value: anti-Pol II CTD S5P (ab5131, abcam)


title: Lung Biopsy, control, THD0002


title: Lung Biopsy, PF, TILD028


title: N2_24h_Clone13_smallRNA

city: Jena

first: Martin

last: Hölzer

state: Thuringia

address: Leutragraben 1

department: Faculty of Mathematics and Informatics

country: Germany

institute: University of Jena

data_processing:
Reference sequence and annotation of the closely related microbat Myotis lucifugus were downloaded from Ensembl (Myoluc2.0, release 86).
We quality trimmed with a Q20 threshold and a window size of length 4 using Prinseq v0.20.3. Reads shorter 15nt were discarded. We used cutadapt v1.8.3 with the prefix TGGAATTCTCGGGTGCCAAG to remove adapters.
We used SortMeRNA (v2.1) to detect and remove ribosomal RNAs.
The quality-controlled and rRNA-depleted reads were mapped to the concatenated reference genomes of M. lucifugus and RVFV using STAR (v2.5.2) with default parameters.
We used featureCounts (v1.5.0) to quantify the mapped reads based on the Ensembl annotation (originally release 86) of M. lucifugus comprising 25,849 genes. Reads were counted strand-specific on exon level and accumulated per gene ID to obtain one count per gene.
Genome_build: Myoluc2.0
Supplementary_files_format_and_content: tab-delimited text files include gene id, chromosome position, orientation, length, and unique raw read counts obtained by featureCounts for each sample

organism: Myotis daubentonii

source_name: kidney

growth_protocol: Immortalized kidney cells from Myotis Daubentonii (MyDauNi) were maintained in DMEM (4,5 g/L) supplemented with 200 µM L-Alanine, 225 µM L-Aspartic acid, 933 µM Glycin, 510 µM L-Glutamic acid, 217 µM L-Proline, 292 µg/L L-glutamine, 184 µM Hypoxanthine, 0,1 mg/L Biotin, 44 mM NaHCO3, 10 % FBS, 10 U/L Penicillin, and 10 µg/L Streptomycin.

extract_protocol:
The medium was removed and the cells washed once in PBS. Total RNA were extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. The samples from each treatment were pooled and the amount of RNA determined using a Nanodrop. The quality and integrity of the respective RNA were deterimend using a Agilent 2100 Bioanalyzer. The samples were then stored at -80°C
RNA libraries were prepared for sequencing using the Illumina TruSeq smallRNA Kit

treatment_protocol: 3×105 MyDauNi cells/well were seeded in a 12-well plate and then incubated 24 h at 37°C, 5% CO2. The following day four wells were mock treated, four wells were treated with 1000 U/ml pan-species interferon-alpha (B/D) and the remaining four wells were infected with RVFV Clone 13 (MOI 5). At 6 and 24 h post-infection samples were taken.

tag: treatment

value: RVFV-clone 13 infection, MOI5, 24h poi

value: immortalized kidney cells

value: MyDauNi


title: N3_24h_Clone13_smallRNA


title: sihnG4-Pol2_S2P

description: Pol II CTD (Ser2) ChIP-seq

treatment_protocol: Transfection with 20 nM hnRNPG siRNA (G4: SI00700084, Qiagen) for 48 hours and crosslinked with 1% formaldehyde

value: anti-Pol II CTD S2P (MABI0602, MBL life science)


title: MSC-P3-H9-1

description: WT

value: WT


title: sihnG4-Pol2_S5P

description: Pol II CTD (Ser5) ChIP-seq


title: A5-PG_1 Sample 17

data_processing:
The quality filtering and adaptor trimming were performed using Cutadapt (v 1.12).
Paired-read alignment for RNA-seq data was carried out against the gene set for C. neoformans var. grubii H99 (CNA3)  excluding non-coding RNAs and mitochondria genes, using STAR (v 2.5.3a).
The expected read count for each gene was computed based on a maximum likelihood estimate, derived from an Expectation Maximization algorithm in RSEM (v1.2.31).
The expected count data were then converted to counts per million (CPM) and normalized by adjusting with the effective library size via the calcNormFactors function implemented in edgeR (v. 3.16.5).
The DEGs were determined by using the negative binomial generalized linear models with quasi-likelihood tests (glmQLFit and glmQLFTest functions in the edgeR package).
Genome_build: CNA3 (GCA_000149245.3)
Supplementary_files_format_and_content: Tab-delimited text files containing expected counts of all genes for all samples.
Supplementary_files_format_and_content: Tab-delimited text files containing FDR P-values of differential gene expression test for each comparison.
Supplementary_files_format_and_content: Tab-delimited text files containing the Log fold-changes of differential gene expression test for each comparison.

extract_protocol:
These lyophilized samples were treated with Trizol and total RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.
Library preparation was prepared by shearing the RNA and adapted for Illumina sequencing using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA).


title: Lung Biopsy, PF, TILD010

tag: disease state


title: sihnG3-Pol2_S5P

description: Pol II CTD (Ser5) ChIP-seq

treatment_protocol: Transfection with 20 nM hnRNPG siRNA (G3: SI00700077, Qiagen) for 48 hours and crosslinked with 1% formaldehyde


title: Lung Biopsy, control, VUHD71


title: N1_24h_Clone13_smallRNA


title: A5-YPD_2 Sample 16

value: yeast extract-peptone-dextrose


title: N3_6h_Clone13_smallRNA

value: RVFV-clone 13 infection, MOI5, 6h poi


title: siC-Pol2_S2P

description: Pol II CTD (Ser2) ChIP-seq


title: A5-YPD_2 Sample 15


title: Lung Biopsy, PF, VUILD64


title: N2_6h_Clone13_smallRNA


title: Lung Biopsy, PF, VUILD63


title: sihnG3-Pol2

description: Pol II ChIP-seq

value: anti-Pol II clone 8WG16 (664912, BioLegend)


title: A5-YPD_1 Sample 14


title: Lung Biopsy, PF, VUILD62-2

value: pulmonary fibrosis (PF)


title: siC-Pol2

description: Pol II ChIP-seq


title: Lung Biopsy, PF, VUILD62-1

value: Lung Biopsy


title: N3_24h_IFN_smallRNA

value: IFN-alpha (1000 U/ml), 24h after treatment


title: sihnG3-Pol2_S2P

description: Pol II CTD (Ser2) ChIP-seq


title: sihnG3-Input

description: Input of ChIP-seq


title: Lung Biopsy, PF, TILD015


title: sihnG4-Input

description: Input of ChIP-seq


title: N2_24h_IFN_smallRNA


title: siC-Input

description: Input of ChIP-seq


title: N1_24h_IFN_smallRNA


title: N3_6h_IFN_smallRNA

value: IFN-alpha (1000 U/ml), 6h after treatment


title: A1-LIM_2 Sample 12

value: starvation-low-iron media

value: Rep 2


title: A1-LIM_1 Sample 9

value: VNI

value: Rep 1


title: Lung Biopsy, PF, VUILD65


title: A1-LIM_2 Sample 11

value: Environment


title: sihnG4-Pol2

description: Pol II ChIP-seq


title: Lung Biopsy, PF, VUILD61-1


title: A1-LIM_1 Sample 10


title: N2_6h_IFN_smallRNA


title: A1-PG_2 Sample 8

value: pigeon guano


title: RGG2-3

description:
diffexpr_wGene_RGG2_WT.txt
diffexprgene_wGene_RGG2_WT.txt

data_processing:
RNA-Seq data was mapped using the STAR computer program version 2.5.3a (PMID 23104886) on the Human genome version NCBI's GRCh37 / UCSC's hg19.
Mapped reads were transformed into exon counts using the featureCounts computer program version 1.6.0 (PMID 24227677).
Exon boundaries definition from the RefSeq database (PMID 26553804), extracted from UCSC's genome table browser for hg19 (PMID 14681465).
Differential expression of exons analyses from exon counts from DEseq2 computer program version 1.20.0 (PMID 25516281).
Simultaneous consideration of biological relevance (fold-change) and statistical significance (P-value) using pi-values (PMID 22321699).
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: diffexpr_wGene_{sample}_WT lists exon expression in {sample} and WT, as well as log2({sample}/WT) and statistical parameters for differential exon expression. diffexprgene_wGene_{sample_WT} lists transcript abundance in {sample} and WT, as well as log2({sample}/WT) and statistical parameters for differential gene expression.

growth_protocol: Human embryonic kidney (HEK) cell line HEK293T/17 was obtained from the American Type Culture Collection (ATCC) and cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose and L-glutamine, without sodium pyruvate (HyClone, SH30022.01) in a 37 °C incubator with a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from HEK293T cells by Trizol (15596026, Thermo) extraction followed by an additional chloroform extraction.
mRNA sequencing libraries were prepared using the Tru-Seq Stranded mRNA LT Sample Prep Kit (RS-122-9005DOC, Illumina).

treatment_protocol: HEK293T cells were transfected with 24 ng/mL of either pCMV3-Flag negative control vector (CV016, Sino Biological) or pCMV3-Flag-RBMX plasmid (WT, RRMmut, RGG1mut, or RGG2mut), as well as 10 nM hnRNPG siRNA (SI00700077, Qiagen), using Lipofectamine 2000 (11668019, Thermo). The cells were collected for RNA extraction 68 hours after transfection.

tag: sirna transfection

value: hnRNPG

tag: plasmid transfection

value: pCMV3-Flag-RBMX RGG2mut

tag: barcode

value: GTCCGC


title: Lung Biopsy, PF, VUILD61-2


title: RGG1-3

description:
diffexpr_wGene_RGG1_WT.txt
diffexprgene_wGene_RGG1_WT.txt

value: pCMV3-Flag-RBMX RGG1mut

value: ATGTCA


title: A5-YPD_1 Sample 13

value: yeast extract-peptone-dextrose


title: N1_6h_Clone13_smallRNA

value: RVFV-clone 13 infection, MOI5, 6h poi

value: immortalized kidney cells

value: MyDauNi


title: N1_6h_IFN_smallRNA


title: RRM-3

description:
diffexpr_wGene_RRM_WT.txt
diffexprgene_wGene_RRM_WT.txt

source_name: RRM, HEK293T/17

value: pCMV3-Flag-RBMX RRMmut

value: CAGATC


title: Lung Biopsy, control, THD0001

value: control

value: Lung Biopsy


title: WT-3

description:
diffexpr_wGene_NCV_WT.txt
diffexprgene_wGene_NCV_WT.txt

value: pCMV3-Flag-RBMX WT

value: GCCAAT


title: N2_24h_mock_smallRNA

value: mock


title: NCV-3

source_name: NCV, HEK293T/17

value: ACAGTG


title: Lung Biopsy, PF, VUILD60-1

value: pulmonary fibrosis (PF)


title: Lung Biopsy, PF, VUILD60-2


title: A1-PG_1 Sample 5

value: VNI

value: Environment

value: pigeon guano

value: Rep 1


title: N3_24h_mock_smallRNA


title: A1-YPD_2 Sample 4

value: yeast extract-peptone-dextrose

value: Rep 2


title: A1-YPD_2 Sample 3


title: Lung Biopsy, PF, VUILD59-1


title: RGG1-2

value: hnRNPG

value: pCMV3-Flag-RBMX RGG1mut

value: AGTCAA


title: Lung Biopsy, PF, VUILD59-2


title: A1-PG_1 Sample 6


title: WT-2

value: GTGAAA


title: RGG2-2

value: pCMV3-Flag-RBMX RGG2mut

value: AGTTCC


title: N1_24h_mock_smallRNA

value: immortalized kidney cells

value: MyDauNi


title: A1-PG_2 Sample 7


title: N2_6h_mock_smallRNA

value: mock


title: N1_6h_mock_smallRNA


title: NCV-2

value: CCGTCC


title: A1-YPD_1 Sample 1


title: A1-YPD_1 Sample 2


title: RRM-2

value: pCMV3-Flag-RBMX RRMmut

value: ACAGTG


title: 72hpfNCC_rep3

city: Charlottesville

first: Sarah

last: Kucenas

state: VA

address: 90 Galderd Dr, Rm 312

department: Biology

institute: University of Virginia

description: Dissassociated neural crest cells

data_processing:
For data quality control, FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases.
After adapter clipping, we removed leading and trailing ambiguous or low quality bases (below Phred quality scores of 3).
Trimmomatic works with a user-defined window spanning the read from 5′ to 3′ and removes bases only at the 3′-end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20, the 3′-end is clipped.
The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: danRer10
Supplementary_files_format_and_content: normalized FPKM counts with annotations

organism: Danio rerio

source_name: Neural crest cells from larval trunk

growth_protocol: Gt(foxd3:mCherry);Tg(sox10:mEGFP) zebrafish embryos were raised in egg water at 28.5C to desired stages

extract_protocol:
Qiagen rneasy micro
Smartseq v4 Ultra Low Input RNA Kit for Sequencing

treatment_protocol: 36 hpf and 72 hpf Gt(foxd3:mCherry);Tg(sox10:mEGFP) embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium-free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS (D-PBS) and then transferred to microcentrifuge tubes along with 100ul D-PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C, 1ml 1x Trypsin with 5% EDTA solution was added, and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D-PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D-PBS+BSA. Three samples of cells (1750 ± 750) at each stage were used for RNA-sequencing.

value: Neural crest cells from larval trunk

tag: transgene

tag: Stage

value: 72 hours post fertilization


title: 72hpfNCC_rep2

description: Dissassociated neural crest cells


title: ZD7

city: Ynagling

first: Shiduo

last: Sun

address: Xinong Rd #22

institute: Northwest A&F University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
The Fragments per Kilobase of transcript per Million mapped reads (FPKM) calculation normalizes read count by dividing it by the gene length and the total number of reads mapped to genes.
TXT file contain fpkm for each sample
Genome_build: sscrofa11.1
Supplementary_files_format_and_content: FPKM

organism: Sus scrofa

source_name: ovary

growth_protocol: The ovaries in our study were collected from sows 4 days post the 4th delivery picked from a commercial sow piggery in Hanshiwei Food Ltd., Co., (Dahua, Guangxi, China), which is negative for PRRSV (porcine reproductive and respiratory syndrome virus) and PCV (porcine circovirus). All sows were slaughtered in a standard slaughterhouse in Xinyouxian Livestock Ltd., Co., (Xining, Guangxi, China), and the left ovaries were quickly taken and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: large litter size (LLS)


title: Lung Biopsy, PF, VUILD58

value: pulmonary fibrosis (PF)

value: Lung Biopsy


title: RGG2-1

value: hnRNPG

value: CAGATC


title: 72hpfNCC_rep1

description: Dissassociated neural crest cells


title: Lung Biopsy, PF, VUILD57


title: ZD5


title: ZD12

value: small litter size (SLS)


title: RGG1-1

value: pCMV3-Flag-RBMX RGG1mut

value: GCCAAT


title: ZD8


title: Lung Biopsy, control, VUHD67

value: control


title: RRM-1

value: CTTGTA


title: 36hpfNCC_rep3

description: Dissassociated neural crest cells

value: 36 hours post fertilization


title: ZD3


title: Lung Biopsy, control, VUHD65


title: 36hpfNCC_rep2

description: Dissassociated neural crest cells


title: NCV-1

value: CGATGT


title: 36hpfNCC_rep1

description: Dissassociated neural crest cells


title: Lung Biopsy, PF, VUILD53


title: N3_6h_mock_smallRNA

value: mock

value: immortalized kidney cells

value: MyDauNi


title: ZD2


title: Lung Biopsy, control, VUHD66


title: WT-1

value: pCMV3-Flag-RBMX WT

value: TGACCA


title: Lung Biopsy, PF, VUILD55


title: BC1807

status: Public on Sep 04 2019

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetermined) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: Serum

tag: metastasis status

value: no-Metastasis

tag: age

tag: er(ps)

tag: pgr(ps)


title: BC1815

description: miRNA


title: BC1781

description: miRNA


title: BC1811

description: miRNA


title: BC1782

description: miRNA


title: BC1795

description: miRNA


title: BC1789

description: miRNA


title: BC1813

description: miRNA


title: BC1808

description: miRNA


title: BC1816

description: miRNA


title: BC1809

description: miRNA


title: BC1800

description: miRNA


title: BC1801

description: miRNA


title: BC1806

description: miRNA


title: BC1776

description: miRNA


title: BC1796

description: miRNA


title: BC1773

description: miRNA


title: BC1799

description: miRNA


title: BC1812

description: miRNA


title: BC1768

description: miRNA


title: BC1755

description: miRNA


title: BC1767

description: miRNA


title: BC1817

description: miRNA

value: Metastasis


title: BC1814

description: miRNA


title: BC1804

description: miRNA


title: BC1818

description: miRNA


title: BC1805

description: miRNA


title: BC1774

description: miRNA


title: BC1802

description: miRNA


title: BC1791

description: miRNA


title: BC1788

description: miRNA


title: BC1770

description: miRNA


title: BC1780

description: miRNA


title: BC1783

description: miRNA


title: BC1784

description: miRNA


title: BC1775

description: miRNA


title: BC1779

description: miRNA


title: BC1766

description: miRNA


title: BC1762

description: miRNA


title: BC1763

description: miRNA


title: BC1764

description: miRNA


title: BC1769

description: miRNA


title: BC1759

description: miRNA


title: BC1758

description: miRNA


title: BC1757

description: miRNA


title: BC1747

description: miRNA


title: BC1753

description: miRNA


title: BC1756

description: miRNA


title: BC1750

description: miRNA


title: BC1752

description: miRNA


title: BC1749

description: miRNA


title: BC1792

description: miRNA


title: BC1742

description: miRNA


title: BC1777

description: miRNA


title: BC1748

description: miRNA


title: BC1746

description: miRNA


title: BC1741

description: miRNA


title: BC1744

description: miRNA


title: BC1740

description: miRNA


title: BC1739

description: miRNA


title: 86

city: Beaverton

first: Don

last: Conrad

state: OR

address: 505 NW 185th Avenue, Mail Code L584

department: Division of Genetics, Oregon National Primate Research Center

institute: Oregon Health & Science University

data_processing:
Standard data processing steps from Genome Technology Access Center (Washington University)
Genome_build: Ensembl_R72
Supplementary_files_format_and_content: tab-delimited text files including count information for each sample

source_name: whole ovary

extract_protocol:
standard RNA extraction using qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: cell type

value: whole ovary

tag: strain

value: WT


title: 214_whole

source_name: whole testis

value: testis

value: whole testis

value: Csmd1 KO


title: BC1737

description: miRNA


title: BC1736

description: miRNA


title: 178_r5

source_name: spermatogonia

value: spermatogonia


title: 308_whole


title: 178_r6

source_name: secondary spermatocyte

value: secondary spermatocyte


title: BC1729

description: miRNA


title: BC1732

description: miRNA


title: BC1735

description: miRNA


title: BC1721

description: miRNA


title: BC1717

description: miRNA


title: BC1727

description: miRNA


title: 286_whole


title: BC1734

description: miRNA


title: 269_whole


title: 178_whole


title: BC1733

description: miRNA


title: 178_r7

source_name: primary spermatocyte

value: primary spermatocyte


title: 286_r4

source_name: spermatid

value: spermatid


title: 178_r4


title: 351_r4


title: 286_r5


title: 544_lr4


title: 648_r6


title: 550_lr7


title: 544_lr7


title: 614_r7


title: KO_24h_2

city: Boston

first: Johannes

last: Wedel

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Bulk RNA-seq of Treg cells

data_processing:
after QC and adapter trimming, alignment was performed using the 2-pass STAR aligner (version 2.6.0a) with the mouse reference genome, mouse_ref_GRCm38.p6
gene expression was quantified using the GENECODE gene model (release M18, gencode.vM18.annotation.gtf) using HTseq-count method with -t transcript -m union options.
counts were normailzed for total read-depth using the DESeq2 method (version 1.16.1) in the R Statistical Computing Environment (version 3.5.1)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include transcripts per million (TPM) values for each sample

source_name: splenocytes

extract_protocol:
CD4+CD25high regulatory T cells were FACS-sorted from spleen of Sh2d2a knock-out mice and sex/age-matched wildtype controls , and subsequently cultured with 1 µg/ml plate-bound anti-CD3 (clone 145-2C11) for up to 24 hours. RNA was isolated usingMyOne Silane Dynabeads and libraries were prepared as previously described (Wedel et al. Am J Transplant. 2019; 19(1):77-88.)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sh2d2a knock-out

tag: cells

value: CD4+CD25high regulatory T cells

tag: condition

value: 24 hours of anti-CD3 stimulation


title: 544_lr5

tag: tissue

tag: genotype


title: 648_r7


title: KO_8h_1

description: Bulk RNA-seq of Treg cells

value: 8 hours of anti-CD3 stimulation


title: KO_24h_1

description: Bulk RNA-seq of Treg cells


title: 648_r5


title: KO_2h_2

description: Bulk RNA-seq of Treg cells

value: 2 hours of anti-CD3 stimulation


title: 648_r4


title: 550_lr6


title: 648_whole


title: 273_whole


title: KO_2h_1

description: Bulk RNA-seq of Treg cells


title: KO_8h_2

description: Bulk RNA-seq of Treg cells


title: WT_24h_2

description: Bulk RNA-seq of Treg cells

value: wild type


title: 613_r7


title: WT_8h_2

description: Bulk RNA-seq of Treg cells


title: WT_2h_1

description: Bulk RNA-seq of Treg cells


title: WT_2h_2

description: Bulk RNA-seq of Treg cells


title: KO_0h_2

description: Bulk RNA-seq of Treg cells

value: no anti-CD3 stimulation


title: KO_0h_1

description: Bulk RNA-seq of Treg cells


title: WT_24h_1

description: Bulk RNA-seq of Treg cells


title: 544_lr6


title: WT_8h_1

description: Bulk RNA-seq of Treg cells


title: WT_0h_2

description: Bulk RNA-seq of Treg cells


title: WT_0h_1

description: Bulk RNA-seq of Treg cells


title: Tre1

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

description: 1_all_miRNA_counts.txt, 2_all_miRNA_TPM.txt, 3_diff_expressed_miRNA.txt

data_processing:
Cutadapt (version 1.14), fastx_toolkit (version 0.0.13) and NGSQCToolkit (version 2.3.3) were used to get clean reads.
Clean reads were matched with Rfam (version 10.0), and rRNA, snRNA, cis-reg, tRNA and other specific sequences were annotated.
The transcripts were filtered using bowtie.
MiRBase (version 22.0) was used for miRNA alignment to annotate known miRNAs.
Novel miRNA prediction of unannotated sequences was performed with miRDeep2. Novel miRNA secondary structure prediction was performed using RNAfold.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The TPM (transcript per million) metric represented the miRNA expression level.

organism: Bos taurus

source_name: bovine in treat group

growth_protocol: Six Holstein cows (n=3, 101±10 DIM, 574±36 kg BW, 32±2 kg milk/d) were utilized in the experimental period while housed in 12 environmentally control chambers and exposed to constant 20°C, 40% humidity.

extract_protocol:
The exoEasy Maxi Kit (no. 76064, QIAGEN) was used for the isolation of serum EVs. miRNeasy Serum/Plasma Kit (no. 217184, QIAGEN) was used to extract EV-miRNAs.
TruSeq Small RNA Sample Prep Kits (no. RS-200-0012, Illumina), Qubit dsDNA Assay Kit (no. Q328520, Life Technologies), Qubit RNA Assay Kit (no. Q32852, Life Technologies), SuperScript II Reverse Transcriptase (no.18064-014, Invitrogen) and DNA loading dye (no.LC6678, Invitrogen) were utilized in this step, following the manufacturer’s instructions. Briefly, 3' adapter and 5' adapter were ligated to the end of the RNA molecules. Then the libraries were reverse transcribed and PCR amplified subsequently. The cDNA constructs were purified and recovered, and the libraries was checked and normalized eventually.

treatment_protocol: Control cows were fed with TMR while treat cows were fed with feed that partly replaced alfalfa hay with whole cotton seed and soybean hull for 30 days.

tag: breed

value: Holstein cow

value: blood

tag: tissue compartment

value: serum extracellular vesicle (EV)

tag: developmental stage

value: mid lactation

tag: diet

value: includes whole cotton seed and soybean hull

tag: Sex

value: female


title: Tre2


title: Tre3


title: Con1

source_name: bovine in control group

value: control (TMR)


title: Con2


title: Con3


title: 1_12: pituitary adenoma

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

data_processing:
1. Counting reads using summarizeOverlaps function form GenomicAlignments package.
2. Differential expression analysis using DEseq2 package.
Genome_build: hg18
Supplementary_files_format_and_content: readcounts_normalized_all.csv contains normalized readcounts for all of the samples.

source_name: pituitary adenoma

extract_protocol:
Two different type of extraction kits were used for RNA isolation from samples: mirVana™ miRNA Isolation Kit [Invitrogen] and QIAamp RNA mini kit [QIAGEN]. MagMAX™ FFPE DNA/RNA Ultra Kit [Applied Biosystems] was used for RNA isolation from FFPE samples.
Ion AmpliSeq™ Transcriptome Human Gene Expression Kit

value: pituitary adenoma

tag: isolation protocol

value: Qiagen

tag: invasivness

value: invasive


title: 20_14: pituitary adenoma


title: 10_13: pituitary adenoma


title: 33_11: pituitary adenoma


title: 40_14: pituitary adenoma


title: 8_14: pituitary adenoma

value: non-invasive


title: 37_14: pituitary adenoma


title: 45_12: pituitary adenoma


title: 67_11: pituitary adenoma


title: NPCs_LDL_48h_rep2

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
Gene expression in adult hippocampal neural precursor cells after 48 h treatment with 100 ug/ul human LDL
LDL2

hyb_protocol: 0.6 ug of Cy3-labeled cRNA (specific activity ≥ 11.8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridised to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (AMADID 028005) for 17 h at 65°C and 10 rpm in a rotating Agilent hybridization oven. After hybridisation, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent). The wash buffers contained 0.005 % Triton X-102.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the AgilentG3_GX-1Color scan protocol for 8x60K high density Microarray Formats (scan area 61x21.6 mm, scan resolution 5 um, dye channel is set to Green and Green PMT is set to 100 %, resulting in 20-bit TIFF images).

data_processing: Raw signal and background intensities were obtained from scanned images with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and grid 028005_D_F_20150604). Data was further processed in R 3.4.4 using the limma package (version 3.34.9). Raw values were background corrected using subtract method and normalized between arrays applying cyclic loess normalization.

source_name: Dentate gyrus of the hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions in the Agilent One-Color Microarray-Based Gene Expression Analysis Manual 6.5. Dye incorporation and cRNA yield were quantified using the NanoDrop ND-1000 spectrophotometer.

growth_protocol: Primary adult hippocampal progenitor cells were isolated from dentate gyri of male 8-weeks old C57BL6/JRj mice and propageted as an adherent monolayer culture on poly-D-lysine/laminin coated dishes in Neurobasal medium (Gibco, Life Technologies) supplemented with 2 % B27 (Invitrogen), 1X GlutaMAX (Life Technologies), 50 units/ml penicillin/streptomycin (Life Technologies) and 20 ng/ml of EGF and bFGF each (PeproTech, Rocky Hill, NJ). Every 2 days, 75% of the culture medium was replaced with fresh medium. Precursor cells were passaged at approximately 80 % confluence by treating with Accutase (PAA Laboratories, Linz, Austria) for 2 minutes, washed with PBS and reseeded at a density of 10^4 cells per cm2.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, Hilden, Germany). The adherent cell cultures were washed once with PBS and then harvested by on-plate lysis with RLT buffer. Lysate was collected using a cell scraper and RNA extracted following the manufacturer’s protocol, including the DNAse step. The concentration and the quality of RNA were analyzed using Eukaryote Total RNA Nano Series Kit 2.6 on the Agilent 210 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cultures grown for 2 days in 6-well plates were subjected to 100 ug/ml LDL or saline as a control and total RNA was isolated 48 later. Three independent experiments were performed.

value: male

value: NPC

tag: agent

value: LDL


title: NPCs_siRNA_non-target_48h_rep2

description:
Gene expression in adult hippocampal neural precursor cells 48 h after transfection with non-targeting siRNA
CTR2

treatment_protocol: Cultures grown for 2 days in 6-well plates in antibiotic-free medium were transfected with a pool of 4 different siRNAs targeting mouse LDLR (ON-TARGETplus SMARTpool, Cat. No. L-048572-00-005, Dharmacon) or non-targetting pool of siRNAs as a conrol. After 24 h, the transfection media was replaced by regular culture media and cells were incubated for further 24 h before harvesting and extraction of total RNA. Three independent experiments were performed.

value: Control


title: NPCs_siRNA_LDLR_48h_rep2

description:
Gene expression in adult hippocampal neural precursor cells 48 h after transfection with LDLR siRNA
LDLRKO2

value: LDLR KD


title: NPCs_LDL_48h_rep1

description:
Gene expression in adult hippocampal neural precursor cells after 48 h treatment with 100 ug/ul human LDL
LDL1


title: NPCs_siRNA_LDLR_48h_rep3

description:
Gene expression in adult hippocampal neural precursor cells 48 h after transfection with LDLR siRNA
LDLRKO3


title: NPCs_siRNA_non-target_48h_rep3

description:
Gene expression in adult hippocampal neural precursor cells 48 h after transfection with non-targeting siRNA
CTR3


title: NPCs_Saline_48h_rep1

description:
Gene expression in adult hippocampal neural precursor cells after 48 h treatment with saline
Saline1


title: BC1745

description: miRNA

value: Serum

tag: metastasis status

value: no-Metastasis

tag: age


title: NPCs_Saline_48h_rep3

description:
Gene expression in adult hippocampal neural precursor cells after 48 h treatment with saline
Saline3


title: NPCs_LDL_48h_rep3

description:
Gene expression in adult hippocampal neural precursor cells after 48 h treatment with 100 ug/ul human LDL
LDL3


title: NPCs_Saline_48h_rep2

description:
Gene expression in adult hippocampal neural precursor cells after 48 h treatment with saline
Saline2


title: NPCs_siRNA_LDLR_48h_rep1

description:
Gene expression in adult hippocampal neural precursor cells 48 h after transfection with LDLR siRNA
LDLRKO1


title: 13_14: pituitary adenoma


title: 36_12: pituitary adenoma


title: 44_12: pituitary adenoma


title: 52_12: pituitary adenoma


title: 38_10: pituitary adenoma


title: 19_08: pituitary adenoma


title: 51_12: pituitary adenoma


title: 16_14: pituitary adenoma

value: mirVana


title: 1_14: pituitary adenoma


title: 10_14: pituitary adenoma


title: 35_12: pituitary adenoma


title: 35_11: pituitary adenoma


title: 4_14: pituitary adenoma


title: 9_13: pituitary adenoma


title: 1_13: pituitary adenoma


title: NPCs_siRNA_non-target_48h_rep1

description:
Gene expression in adult hippocampal neural precursor cells 48 h after transfection with non-targeting siRNA
CTR1


title: 26_14: pituitary adenoma


title: 80_11: pituitary adenoma


title: 37_12: pituitary adenoma


title: 57_14: pituitary adenoma


title: 55_14: pituitary adenoma


title: 5_13: pituitary adenoma


title: 51_10: pituitary adenoma


title: 46_12: pituitary adenoma


title: 17_12: pituitary adenoma


title: 38_12: pituitary adenoma


title: 4P_FFPE: pituitary gland

source_name: pituitary gland

value: pituitary gland

value: MagMax

value: control


title: 15_13: pituitary adenoma


title: 17_13: pituitary adenoma


title: 3P_FFPE: pituitary gland


title: 26_10: pituitary adenoma


title: HiC_MJ6_wt_5A1_noco

first: Geoffrey

last: Fudenberg

address: 1650 Owens

department: Data Science and Biotechnology

institute: Gladstone Institutes

description: mitotic

data_processing:
HiC-pro (Servant et al., Genome Biology, 2015, 16:259, DOI 10.1186/s13059-015-0831-x) with mapping to SK1Mod (Crawford et al., bioRxiv 496182; doi: https://doi.org/10.1101/496182) genome and with parameters for DpnII and binned to 2 and 5 kb
Genome_build: SK1MOD (Crawford et al., bioRxiv 496182; doi: https://doi.org/10.1101/496182)
Supplementary_files_format_and_content: HiC-pro sparse matrices, bed file is from the default output of the Hi-C-pro pipeline, and shows the chromosomal positions of bins in the sparse matrices.

organism: Saccharomyces cerevisiae

source_name: Hi-C, wt, mitotic growth, arrested in G2/M with nocodazole, biological replicate 2

growth_protocol: S. cerevisiae diploid SK1 cells were grown in YPD (1% Yeast extract, 2% Peptone, 2% Glucose) to saturation for meiotic timecourses and into exponential phase for mitotic experiments.

extract_protocol:
For meiotic samples: 5 ml aliquots (20-30 ODs) of S. cerevisiae diploid SK1 cells were fixed with Formaldehyde at 3% final concentration for 20 minutes at 30 °C, 250 rpm, then quenched by incubating with a final concentration of 0.35 M Glycine (2x the volume of Formaldehyde added) for an additional 5 minutes. Cells were washed with water, split into two samples and stored at -80 ̊C ready for library preparation. For mitotic samples: 100ml (50-80 OD) of S. cerevisiae diploid SK1 cells were fixed with Formaldehyde as described above and used for one library.  The Hi-C protocol used was amended from Belton and Dekker (2015, Cold Spring Harb Protoc; doi:10.1101/pdb.prot085209) by ~5-fold reduction in all materials and volumes. Briefly, cells were thawed, washed in spheroplasting buffer (SB, 1 M Sorbitol, 50 mM Tris pH 7.5) and digested for 15-20 min at 35 ˚C with 100 micrograms/ml 100T Zymolyase in SB containing 1% beta-Mercaptoethanol. Cells were washed in restriction enzyme buffer, chromatin was solubilised by adding SDS to 0.1% and incubating at 65 ˚C for 10 minutes. Excess SDS was quenched by addition of Triton X100 to 1%, and chromatin was incubated with 2.07U/ul of DpnII overnight at 37 ˚C. DNA ends were filled-in with nucleotides, substituting dCTP for biotin-14-dCTP using Klenow fragment DNA polymerase I at 37 ˚C for 2 h followed by addition of SDS to 1.5% and incubation at 65 ˚C for 20 minutes to inactivate Klenow and further solubilise the chromatin. The sample volume was diluted 15-fold, crosslinked DNA ends ligated at 16 ˚C for 8 h using 0.024U/ul of T4 DNA ligase, and crosslinks reversed by overnight incubation at 65 ˚C in the presence of proteinase K. DNA was precipitated with ethanol, dissolved in TE and passed through an Amicon 30 kDa column. DNA was further purified by phenol:chloroform:isoamylalcohol extraction and precipitated again before treating with RNaseA at 37 ˚C for 1 h. Biotin was removed from unligated ends by incubation with T4 DNA polymerase at 20˚C for 4 h and at 75 ˚C for 20 minutes for inactivation of the enzyme. DNA was subsequently fragmented using a Covaris M220 (Duty factor 20%, 200 cycles/burst, 350s, 20 ˚C). After purification with with Qiagen MinElute Columns, DNA ends were repaired using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I at 20˚C for 30 minutes. The DNA was purified with Qiagen MinElute Columns and 3’ ends were A-tailed with dATP using Klenow Fragment (exo-) at 37˚C for 30 min and then at 65˚C for 20 min to inactivate the enzyme.
The Hi-C protocol used was amended from Belton and Dekker (2015, Cold Spring Harb Protoc; doi:10.1101/pdb.prot085209) by ~5-fold reduction in all materials and volumes. Briefly, the end-repaired and A-tailed fragments were fractionated using a Blue Pippin (Sage) and the 100-250bp fraction was used for further processing. Biotinylated fragments were enriched using streptavidin magnetic beads (C1) and NextFlex (Bioo Scientific) barcoded adapters were ligated while the DNA was on the beads. Resulting libraries were minimally amplified by PCR and sequenced using paired-end 42 bp reads on a NextSeq500 (Ilumina; Brighton Genomics).

treatment_protocol: For meiotic samples: S. cerevisiae diploid SK1 cells were synchronised in G1 by growth at 30 ˚C for 16-18 h in 30 ml YPA (1% Yeast extract, 2% Peptone, 1% KAc) to OD600 of ~4, harvested, washed, and resuspended in prewarmed sporulation medium (2% KAc with 0.2x nutritional supplements). 5 ml aliquots (20-30 ODs, sufficient for 2 Hi-C libraries) of relevant meiotic timepoints were collected. For mitotic samples: S. cerevisiae diploid SK1 cells were grown in YPD (1% Yeast extract, 2% Peptone, 2% Glucose) to exponential phase, 10 micrograms/ml of nocodazole were added and 100ml of cells (50-80 OD, sufficient for 1 Hi-C library) were harvested after 2h.

tag: background strain

tag: phenotype

value: mitotic


title: 50_12: pituitary adenoma


title: HiC_SSY49_ndt80Dhop1D_1A_8h

description: hop1 ndt80

source_name: Hi-C, ndt80 and axial element of the synaptonemal complex mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 1

value: ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG/", nuc1::LEU2/", his4X::LEU2/", hop1::LEU2/", ndt80delta::LEU2/"

value: hop1 ndt80


title: HiC_SSY25_ndt80Dzip1D_1B2_8h

description: zip1 ndt80

source_name: Hi-C, ndt80 and transverse filament of the synaptonemal complex mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 1

value: ho::LYS2/", lys2/", ura3/', arg4-nsp/", leu2::hisG/", his4X::LEU2/", nuc1::LEU2/", zip1::LEU2/", ndt80delta::LEU2/"

value: zip1 ndt80


title: 2P_FFPE: pituitary gland


title: HiC_SSY58_ndt80Drec8D_2A_8h

description: rec8 ndt80

source_name: Hi-C, ndt80 and cohesin mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 2

value: ho::LYS2/", lys2/", ura3/", leu2::hisG/", nuc1::LEU2/", arg4-nsp/", rec8::KanMX/", ndt80delta::LEU2/"

value: rec8 ndt80


title: HiC_SSY25_ndt80Dzip1D_2A_8h

description: zip1 ndt80

source_name: Hi-C, ndt80 and transverse filament of the synaptonemal complex mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 2


title: 1P_FFPE: pituitary gland


title: HiC_SSY20_ndt80Drec8D_1A2_8h

description: rec8 ndt80

source_name: Hi-C, ndt80 and cohesin mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 1

value: ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG/", rec8delta::KanMX4/", ndt80delta::LEU2/"


title: 37_10: pituitary adenoma

value: pituitary adenoma

value: non-invasive


title: HiC_SSY14_ndt80D_1A1_8h

source_name: Hi-C, ndt80 mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 1

value: ho::LYS2/", lys2/", ura3/", arg4-nsp/", leu2::hisG/", his4X::LEU2/", nuc1::LEU2/", ndt80delta::LEU2/"


title: 24_14: pituitary adenoma


title: 44_14: pituitary adenoma

value: invasive


title: HiC_SSY14_ndt80D_1A_4h

source_name: Hi-C, ndt80 mutant, meiotic timecourse 4h


title: HiC_SSY14_ndt80D_1A2_0h

source_name: Hi-C, ndt80 mutant, meiotic timecourse 0h/G1


title: HiC_SSY14_ndt80D_2A2_8h

source_name: Hi-C, ndt80 mutant, meiotic timecourse 8h, arrested in pachytene, biological replicate 2


title: 14_12: pituitary adenoma


title: HiC_MJ6_wt_3A_6h

description: Wild type

source_name: Hi-C, wt, meiotic timecourse2 6h

value: Wild type


title: pifq_rep2

city: Wuhan

first: xiaodan

last: yu

state: Hubei Province

address: No.1,Shizishan Street · Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

data_processing:
Casava1.8.2 software was used for basecalling.
Trimmomatic and/or fastx_clipper were used to remove adapters. Poor quality bases (less than Phred-20) were removed (clipped) from both the 5' and 3' ends of the Unaligned reads. After adapter removal and quality clipping any reads below a minimum (30 bases) length were discarded. Reads were then mapped to TAIR10 assembly of the Arabidopsis genome using Tophat v2.1.0 with default parameters.
Digital gene expression (counts) was determined for each sample using HTSeq-count v0.6.1 (Anders et al., 2015) with the following parameters: -s reverse -r pos -m intersection-nonempty -t exon -i gene_id.
Differential expression analysis was performed using the edgeR package as follows: edgeR analysis began with a count table comprising 33,602 genes. Genes expressed at low levels were then filtered out by removing any genes for which there was not at least 1 count per million in at least four of the samples. This resulted in a list of 18,842 expressed genes. Counts were then normalized using TMM normalization. Next, the “ANOVA-like” procedure in EdgeR was used to identify genes that were differentially expressed between any of the genotypes (FDR < 0.05). This resulted in a list of 14,688 differentially expressed genes. To determine which of these genes were differentially expressed in each of the mutants compared to wild type, the exact test for the negative binomial distribution (Robinson and Smyth, 2008) was used followed by a Bonferroni correction to maintain a gene-wise error rate of 0.05
Genome_build: Tair10
Supplementary_files_format_and_content: tab-delimited text files include counts values or normalized count values for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: After surface-sterilizing, the seeds were stratified at 4 °C for 3 d in darkness.The seeds were irradiated with continuous white light for 12h,and then placed in the dark and at 22°C for 4 days before havresting.

extract_protocol:
4-day-old dark-grown seedlings were ground into powder in liquid nitrogen, and total RNA was extracted by using the RNeasy Plant Mini Kit(QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: post germinal day 4

tag: growth condition

value: grown in the dark for 4 days, at 22°C .

value: pifq1 pifq3 piq4 pifq5 homozygote


title: HiC_MJ6_wt_3A_4h

description: Wild type

source_name: Hi-C, wt, meiotic timecourse2 4h


title: HiC_MJ6_wt_4A1_noco

description: mitotic

source_name: Hi-C, wt, mitotic growth, arrested in G2/M with nocodazole, biological replicate 1


title: HiC_MJ6_wt_3A_3h

description: Wild type

source_name: Hi-C, wt, meiotic timecourse2 3h


title: pifq_rep1


title: f1f3_rep2

value: fypp1 fypp3 homozygote


title: HiC_MJ6_wt_3A_2h

description: Wild type

source_name: Hi-C, wt meiotic timecourse2 2h


title: L002_small RNA seq

city: Göttingen

first: Nicolas

last: Lemus-Diaz

state: Lower Saxony

address: Humboldtalle 23, 37073 Goettingen, Germany

institute: Goettigen University Medical Center

data_processing:
Raw reads were trimmed and quality filtered employing the Ion -Torrent Suite Software (Life Technologies, CA, USA).
FASTQ outputs from the suite were changed to FASTA format and collapsed using FASTX-toolkit (http://hannonlab.cshl.edu/);
collapsed FASTA files were aligned to the miRbase v 2188 and snoRNA base v3 89 with Bowtie290 employing the following command line arguments:  -D 15 -R 3 -N 0 -L 16 -k 20 --local -i S,1,0.50 --score-min L,18,0 --ma 1 --np 0 --mp 2,2 --rdg 5,1 --rfg 5,1
The rawdata.txt file contains the overall read count for individual miRNA and snoRNAs. Text files contain a the read length, location over the snoRNA gene (start and end position), and the number of identical reads found in each library. Files are sorted by snoRNA class and library.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Raw align reads to snoRNA database and miRbase 21

source_name: Human embryonic kidney 293 cells

growth_protocol: HEK293 cells were cultivated in Dulbecco´s modified Eagle’s Medium (DMEM). Cell culture media were supplemented with 10% foetal bovine serum and 1% antibiotics (Penicillin and Streptomycin)

extract_protocol:
Total RNA was isolated using Phenol/Chloroform extraction
Total Isolated RNA was analysed for quality and quantity using BioAnalyzer System . Total RNA (2 μg) was purified with the magnetic bead clean-up module  for small RNAs. Small RNA was ligated with sequencing adapters, reverse transcripted and purified (Ion Total RNA-Seq Kit v2). Finally, barcodes were added, and library size and amount were detected via BioAnalyzer HS Chip (Agilent, Santa Clara, USA).

tag: cell line

tag: cell type

value: Human embryonic kidney cells

tag: molecule subtype

value: small RNA


title: f1f3_rep1

tag: genotype


title: COL_rep2


title: HiC_MJ6_wt_2A1_6h

city: San Francisco

description: Wild type

source_name: Hi-C, wt meiotic timecourse1 6h


title: 286_r6

source_name: secondary spermatocyte

tag: tissue

value: testis

value: secondary spermatocyte

tag: strain

value: Csmd1 KO


title: COL_rep1

tag: developmental stage


title: HiC_MJ6_wt_2A1_5h

description: Wild type

source_name: Hi-C, wt meiotic timecourse1 5h


title: HiC_MJ6_wt_2A_4h

description: Wild type

source_name: Hi-C, wt meiotic timecourse1 4h


title: L003_small RNA seq


title: HiC_MJ6_wt_2A_3h

description: Wild type

source_name: Hi-C, wt meiotic timecourse1 3h


title: B9 E2+MPA+cAMP _ day 12 for Patient H8_replicate3

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description:
replicate3
readcount.txt

data_processing:
Raw sequences (fastq) were subjected to quality control using windowed adaptive quality triming approach implemented in fqtrim (https://ccb.jhu.edu/software/fqtrim/).
Read quallity was checked by FastQC and quality control was performed by fqtrim.
The quality reads were then mapped to the human reference genome (GRCh38) using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/).
Read counts mapping to each gene were determined from the mapping data using FeatureCounts
Differential expression analysis between sample groups was performed by robustly fitting the expression data to a generalized linear model using edgeRrobust
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-limited text file of read count data.

source_name: uterine organoids

growth_protocol: We used the protocol of Matrigel and WNT-activating conditions to generate three-dimensional human uterine gland organoid (HUGO) cultures from endometrial biopsies.

extract_protocol:
Total RNA was extracted from hormone-treated organoids using a standard TRIzol-based protocol and Direct-zol RNA MiniPrep Plus isolation kit (Zymo Research, R2070). To eliminate genomic DNA contamination, isolated RNA was treated with DNase I (RNase-Free DNase Set (Qiagen, 79256).
RNA library preparation and sequencing was conducted by Novogene, California.

treatment_protocol: After passage, HUGO were grown for 4 days in expansion medium and then treated with estrogen (E2) for 2 days and then either nothing (Control), E2 and medroxyprogesterone acetate (MPA) or E2+MPA+cAMP for a further 6 days (n=3 replicates per patient and treatment).

tag: treatment

tag: days of culture

tag: patient id

value: Patient H8


title: A6 Estrogen _ day 6 for Patient H7_replicate3

description:
replicate3
readcount.txt

value: Estrogen

value: Patient H7


title: L001_small RNA seq


title: HiC_MJ6_wt_2A1_2h

description: Wild type

source_name: Hi-C, wt meiotic timecourse1 2h


title: A12 E2+MPA _ day 12 for Patient H7_replicate3

description:
replicate3
readcount.txt


title: B6 E2+MPA _ day 12 for Patient H8_replicate3

description:
replicate3
readcount.txt