title: RNA_4h_r5

description: processed data file: salmonquant.out

extract_protocol:
Cells were collected by filtration and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alcohol isolation. PolyA selection was performed with 100 ug of RNA and oligo-dT DynaBeads.
The RNA-seq libraries were prepared using the NEXTflexTM Rapid Directional mRNA-Seq Kit (Bioo Scientific) according to manufacturer’s instructions. 100 ng of poly-A selected mRNA was used for all libraries. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.


title: Ume6_IP_r3

status: Public on Nov 01 2020

type: SRA

city: Berkeley

first: Amy

middle: Moreda

last: Tresenrider

state: CA

address: 628 Barker Hall

department: Molecular and Cell Biology

country: USA

institute: UC Berkeley

description:
processed data file: Ume6-IP-R3_rand_diffbind-narrow_0.001_FE.bw
processed data file: Ume6-IP-R3_rand_diffbind-narrow_0.001_peaks.narrowPeak

library_source: genomic

data_processing:
The processing steps for each type of data is outlined in our methods section.
Genome_build: SK1 budding yeast genome published in PMID 28416820 (SK1.cds.fa, SK1.all_feature.gff).
Supplementary_files_format_and_content: bigWig, narrowPeak, txt, csv

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: BYTA

growth_protocol: Yeast cells were prepared for meiosis as described in our methods section.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen. Cells were lysed by bead beating, the chromatin was sheared by sonication, and protein-DNA fragments of interest were isolated with a specific antibody and magnetic protein A Dynabeads.
Libraries were prepared as instructed by the ThruPLEX DNA-seq Kit (R400427, Takara). 0.5-1 ng of starting material was used with 11 rounds of PCR. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.

treatment_protocol: To induce entry into meiosis, after 2 hours in SPO, cells were treated with 50 𝜇M CuSO4.

tag: strain

tag: ploidy

value: diploid

tag: chip antibody


title: RNA_2h_r5

description: processed data file: salmonquant.out

library_source: transcriptomic

molecule: polyA RNA

source_name: SPO 2h

tag: stage of meiosis

value: premeiotic (2h in SPO)


title: Ume6_IP_r1

description:
processed data file: Ume6-IP-R1_rand_diffbind_narrow_0.001_FE.bw
processed data file: Ume6-IP-R1_rand_diffbind_narrow_0.001_peaks.narrowPeak


title: TL_4h_R5

description:
processed data file: 181130TL_de_counts_all_genes.csv
processed data file: 181130_luti_and_orf_peaks_with_counts.csv
processed data file: 190408TL_de_counts_all_genes.csv
processed data file: 190408_luti_and_orf_peaks_with_counts.csv

data_processing:
Library strategy: TL-seq
The processing steps for each type of data is outlined in our methods section.
Genome_build: SK1 budding yeast genome published in PMID 28416820 (SK1.cds.fa, SK1.all_feature.gff).
Supplementary_files_format_and_content: bigWig, narrowPeak, txt, csv

source_name: SPO 4h

extract_protocol:
Cells were collected by filtration and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alcohol isolation. PolyA selection was performed with 100 ug of RNA and oligo-dT DynaBeads.
The 5’ end sequencing approach was performed as in (Wu et al., 2018). See methods for details.

value: meiotic prophase (4h in SPO)


title: TL_4h_R4

description:
processed data file: 190408TL_de_counts_all_genes.csv
processed data file: 190408_luti_and_orf_peaks_with_counts.csv


title: RNA_4h_r4

description: processed data file: salmonquant.out


title: H3K4me2_4h_r3

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K4me2_4h_ab_R3_diffbind_narrow_FE.bw


title: RNA_2h_r4

description: processed data file: salmonquant.out


title: H3K36me3_2h_r3

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_2h_ab_R3_diffbind_narrow_FE.bw

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen. Cells were lysed by bead beating, the chromatin was sheared by sonication, and protein-DNA fragments of interest were isolated with a specific antibody and magnetic protein A Dynabeads.
Libraries were prepared as instructed by the ThruPLEX DNA-seq Kit (R400427, Takara). 15 ng of starting material was used with 7 rounds of PCR. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.


title: input_4h_r3

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_4h_ab_R3_diffbind_narrow_FE.bw
processed data file: H3K4me2_4h_ab_R3_diffbind_narrow_FE.bw

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen. Cells were lysed by bead beating, the chromatin was sheared by sonication.
Libraries were prepared as instructed by the ThruPLEX DNA-seq Kit (R400427, Takara). 15 ng of starting material was used with 7 rounds of PCR. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.


title: Ume6_in_r2

description:
processed data file: Ume6-IP-R2_rand_diffbind_narrow_0.001_FE.bw
processed data file: Ume6-IP-R2_rand_diffbind_narrow_0.001_peaks.narrowPeak


title: input_2h_r3

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_2h_ab_R3_diffbind_narrow_FE.bw
processed data file: H3K4me2_2h_ab_R3_diffbind_narrow_FE.bw


title: H3K4me2_2h_r3

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K4me2_2h_ab_R3_diffbind_narrow_FE.bw


title: H3K4me2_4h_r2

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K4me2_4h_ab_R2_diffbind_narrow_FE.bw


title: DMD2 1

status: Public on Nov 24 2020

city: Newark

first: Gopal

middle: J.

last: Babu

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers NJMS

data_processing:
bases were trimmed to a minimum phred quality score of 25 and Partek Filter contaminans was used to filter rDNA and mtrDNA
reads were aligned to STAR 2.6.1 mm10 genome build
reads were normalized to a 1+ log(TMM ) format and all transcripts with an abundance of less than 1 were removed
Partek remove batch effect was used to mitigate the statistical effect of total reads present on sampleheterogeneity
PARTEK GSEA, a version of LIMMA, was used to identify differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: txt files

molecule: total RNA

organism: Mus musculus

growth_protocol: mice were reared until the age of 6 months old

extract_protocol: RNA extraction from mouse LV was done with standard kit

treatment_protocol: wt, mdx, and mdx sln+/-  mice were examined

tag: genotype

value: mdx

tag: tissue

value: Left ventricle

tag: age

value: 6 month old

value: C57 genetic background


title: input_2h_r2

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_2h_ab_R2_diffbind_narrow_FE.bw
processed data file: H3K4me2_2h_ab_R2_diffbind_narrow_FE.bw


title: TL_2h_R4


title: H3K4me2_2h_r2

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K4me2_2h_ab_R2_diffbind_narrow_FE.bw


title: H3K36me3_4h_r2

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_4h_ab_R2_diffbind_narrow_FE.bw


title: H3K4me2_4h_r1

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K4me2_4h_ab_R1_diffbind_narrow_FE.bw


title: input_4h_r2

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_4h_ab_R2_diffbind_narrow_FE.bw
processed data file: H3K4me2_4h_ab_R2_diffbind_narrow_FE.bw


title: H3K36me3_4h_r1

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_4h_ab_R1_diffbind_narrow_FE.bw


title: MNase_4h_r6

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_4h_R6_CPM.bw

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen.
Cells were spheroblasted with zymolase and the DNA was digested with MNase as in (Rodriguez et al. 2014) with minor modifications as outlined in our methods.


title: MNase_4h_r4

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_4h_R4_CPM.bw


title: H3K36me3_2h_r1

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_2h_ab_R1_diffbind_narrow_FE.bw


title: H3K36me3_2h_in_r1


title: H3K4me2_2h_r1

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K4me2_2h_ab_R1_diffbind_narrow_FE.bw


title: MNase_2h_r6

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_2h_R6_CPM.bw


title: H3K4me2_2h_in_r1

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen. Cells were lysed by bead beating, the chromatin was sheared by sonication.
Libraries were prepared as instructed by the ThruPLEX DNA-seq Kit (R400427, Takara). 0.5-1 ng of starting material was used with 11 rounds of PCR. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.


title: MNase_2h_r4

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_2h_R4_CPM.bw


title: MNase_4h_B

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_4h_R1_CPM.bw


title: MNase_2h_B

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_2h_R1_CPM.bw


title: E95_Cortex_neurosphere

status: Public on Oct 01 2020

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

data_processing:
Data of RNA-seq (fastq file format) were quality-checked, and low-quality reads (score < 30), adapter sequences, and overrepresented sequences such as poly-A chain were trimmed using the Trim Galore! (ver.0.4.0).
The remaining reads were mapped to the Callithrix jacchus genome (cj3.2.1.86) using the STAR (ver.2.5.3a), and the output file (BAM file format) were summarized using the featureCounts (1.5.2).
Genome_build: cj3.2.1.86
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Callithrix jacchus

source_name: Embryo-derived neurospheres

growth_protocol: See the citation

extract_protocol:
RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: See the citation

tag: cell type

value: Embryo-derived neurospheres


title: H3K36me3_2h_r2

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_2h_ab_R2_diffbind_narrow_FE.bw


title: MNase_2h_G

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_2h_R3_CPM.bw


title: CM421F_B0_12_iPS_P11

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: Ped_Tissue_patient7corpusCF_repl1

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with htseq-count 0.9.1 by using cellRanger pre-build genes annotations (Ensembl Assembly 93)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

organism: Homo sapiens

source_name: Pediatric tissue from stomach mucosa, corpus, cystic fibrosis

growth_protocol: Cell were passaged every 6-8 days. To passage the organoids, Matrigel droplets were disrupted by pipetting in the well and transferred to tubes on ice. Cells were washed with 10 mL of cold basal ADMEM+++ and centrifuged at 200 g at 4°C. (First method) For single cell dissociation, supernatant was discarded, and the pellet resuspended in 1 mL of TrypLE (Thermo Fisher) and incubated for 5 min. After incubation organoids were disaggregated by pipetting, and 10 mL of ice-cold ADMEM+++ was added to dilute and inhibit TrypLE. (Second method) For standard organoid passage during expansion, the organoid pellet was resuspended in 1.5 mL of ice-cold ADMEM+++ and organoids were manually disrupted by narrowed (flamed) glass pipette pre-coated in BSA 1% in PBS, to avoid adhesion to the glass. Cells were washed, pelleted and supernatant discarded. Almost-dry pellets of disaggregated organoids (or single cells) were thoroughly resuspended in cold liquid Matrigel, aliquoted in 30 µL droplets in pre-warmed multi-well plates and incubated at 37C for 20 min to form a gel. Rho-kinase inhibitor (Tocris) was added to single cell dissociated organoids. Medium was added and changed every 3 days.

extract_protocol:
For RNA isolation from stomach tissues, i) pediatric stomach biopsies consisted of only mucosal layer from surgical samples; ii) Late fetal stomachs were cut open and mucosal layer was isolated; iii) early fetal stomachs were processed with no layer isolation, given the small size of the samples. Mucus was removed from all the samples with a glass coverslip to prevent RNA loss during the isolation protocol, and tissues washed in ice-cold PBS. Then the tissues were finely cut with a scalpel on a Petri-dish on ice and transferred to 1.5 mL tubes. RNA was isolated from cultured organoids in Matrigel with 30 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Cells were then washed in ice cold PBS to remove matrix leftovers that could interfere with RNA isolation. Organoids were centrifuged at 200 g at 4°C and supernatant discarded. Dry pellets of tissues and organoids were lysed with RLT buffer (Qiagen). RNA was isolated with RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from  total RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following manufacturer protocol

treatment_protocol: All organoid lines are expanded in the same WENR culture medium, with no different treatment protocol among them

tag: passage

value: not applicable

tag: culture method


title: H3K4me2_4h_in_r1


title: H3K36me3_4h_in_r1


title: FB_E13.5

status: Public on Oct 05 2020

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

data_processing:
All scripts are available in https://github.com/lldelisle/scriptsForFernandezGuerreroEtAl2020
Adapters and bad-quality bases were removed with Cutadapt version 1.16 options -m 15 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30.
Reads were further mapped using bowtie2 version 2.3.5 options --very-sensitive --no-mixed –no-discordant --dovetail -X 1000.
Only pairs with MAPQ30, concordant and in chromosomes which are not chrM were kept. Duplicates were removed with picard and the bam file was converted to bed with bedtools.
Peak calling and coverage were obtained with macs2 version 2.1.1.20160309 with options --nomodel --keep-dup all --shift -100 --extsize 200.
For each dataset, summit positions were extended 500bp each side and merged and the number of reads falling into these regions was used to normalize the coverage.
Mean of normalized coverage was performed between duplicates of ectoderm samples
Genome_build: mm10
Supplementary_files_format_and_content: bw: for each sample, the coverage from macs2 (not normalized)
Supplementary_files_format_and_content: normalized_ATAC_E13_FB.bw: normalized coverage for the forebrain E13.5 sample
Supplementary_files_format_and_content: normalized_*_neq2.bw : mean of normalized coverage
Supplementary_files_format_and_content: narrowPeak.gz : narrowPeak from macs2

source_name: Forebrain

extract_protocol:
For E14.5 ectoderm samples, the ectoderms were first isolated from the subjacent mesoderm by trypsin digestion and then dissociated to single cell suspension by pipetting up and down. For E13.5 forebrain sample, skull cartilage was removed with forceps and the forebrain portion was removed. The sample was digested in PBS with 10% FCS and digested with collagenase at 37ºC at 400rpm for 20 minutes.
ATAC-seq was performed as described in Buenrostro et al., 2016.

tag: developmental stage

value: Forebrain


title: Ped_Tissue_patient3corpusGC_repl3

source_name: Pediatric tissue from stomach mucosa, corpus, gastric closure


title: MNase_4h_G

description:
processed data file: 4hrfiles-2hrfiles.positions.integrative.txt
processed data file: 130-170_MN_4h_R3_CPM.bw


title: Ped_Tissue_patient4corpus_repl1

source_name: Pediatric tissue from stomach mucosa, sorpus


title: Ped_Tissue_patient5corpus_repl1

source_name: Pediatric tissue from stomach mucosa, corpus


title: Ped_Tissue_patient5antrum_repl1

source_name: Pediatric tissue from stomach mucosa, antrum


title: Ped_Tissue_patient3antrum_repl1


title: Fet_Tissue_W15_repl2

source_name: Fetal tissue from stomach mucosa and submucosa (PCW 15)


title: Fet_Tissue_W10_repl1

source_name: Fetal tissue from stomach mucosa and submucosa (PCW 10)


title: Fet_Tissue_W15_repl1


title: Fet_Tissue_W11_repl1

source_name: Fetal tissue from stomach mucosa and submucosa (PCW 11)


title: Ped_Tissue_patient3corpus_repl1


title: Ped_Tissue_patient6corpus_repl1


title: Fet_Org_W11_repl1

source_name: Cultured organoid from fetal stomach tissue (PCW 11)

value: P 6

value: Split at single cells with TrypLE; plated in 30 uL droplets of Matrigel Growth Factor Reduced; expanded for 8 days in gastric culture medium WENR (wnt, egf, noggin, r-spondin); isolated from Matrigel using 20 min of ice cold Cell Release Solution ECM digestion; RNA extracted in RLT buffer.


title: Fet_Tissue_W17_repl1

source_name: Fetal tissue from stomach mucosa (PCW 17)


title: Fet_Tissue_W20_repl1

source_name: Fetal tissue from stomach mucosa (PCW 20)


title: Fet_Org_W11_repl2


title: Fet_Org_W11_repl3


title: Fet_Org_W8_repl4

source_name: Cultured organoid from fetal stomach tissue (PCW 8)


title: Fet_Tissue_W20_repl2


title: Fet_Tissue_W17_repl2


title: Fet_Org_W11_repl4


title: Fet_Tissue_W18_repl1

source_name: Fetal tissue from stomach mucosa (PCW 18)


title: Fet_Org_W8_repl3


title: Fet_Org_W8_repl2


title: Fet_Tissue_W18_repl2


title: Fet_Org_W8_repl1


title: Fet_Org_W20_repl3

source_name: Cultured organoid from fetal stomach tissue (PCW 20)


title: Fet_Org_W20_repl4


title: Fet_Org_W20_repl1


title: Fet_Org_W18_repl2

source_name: Cultured organoid from fetal stomach tissue (PCW 18)

value: P 9


title: Fet_Org_W18_repl3


title: Ped_Org_patient2_repl2

source_name: Cultured organoid from pediatric stomach tissue


title: Ped_Org_patient2_repl4


title: Fet_Org_W18_repl1


title: Fet_Org_W18_repl4


title: Ped_Org_patient2_repl3


title: Ped_Org_patient1_repl3


title: Fet_Org_W20_repl2


title: Ped_Org_patient1_repl4


title: Ped_Org_patient2_repl1


title: Ped_Org_patient1_repl2


title: Ped_Org_patient1_repl1


title: 20w_minus_1

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with RSEM 1.3.0 by using gencode pre-build genes annotations (hg38 primary assembly)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include expected counts for each sample as output from RSEM

growth_protocol: Fully grown gastric organoids at day 7 after single cell disaggregation were removed from surrounding extracellular matrix using a modified published protocol. Matrigel was dissolved with 60 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Organoids were retrieved from the plates using 1% BSA-coated cut-end tips and transferred to 1% BSA-coated 15 mL tubes. Cells were extensively washed with ice-cold PBS and centrifuged at 200 g for 5 min at 4°C. Supernatant was discarded, the pellet was resuspended in complete medium and transferred to non-tissue culture treated low-adhesive multiwell plates (pre-coated in 1% BSA). Organoids were cultured in suspension for 3 days to allow reversion of polarity, before use in infection experiments.

extract_protocol:
Pelletted organoids were extracted in RLT buffer
cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following manufacturer suggested protocol. cDNA generated with SMART-Seq v4 Kit were used for preparation of library with NEXTERA XT DNA Library Preparation kit, following the suggested protocol.

treatment_protocol: Reversed-polarity organoids were infected at a MOI of 1 by incubation with 250 µl of an expansion medium viral suspension for 2 hours. After infection, organoids were washed twice in DMEM to remove unbound virus. RP-GOs were dispersed in a 400 µl expansion medium at 37 °C with 5% CO2. For all organoid cultures 50 µl of supernatant were harvested at 0, 24, 48, and 72 hours post infection. An equal volume of expansion medium replaced the sampled supernatant at each collection time. An extra sample at 96 hours post infection was collected for the RP-GOs. Samples were stored at -80°C before titration through the FFA.

tag: agent

value: negative paired control


title: 20w_minus_2


title: 20w_plus_1

value: SARS-CoV-2 infected at MOI 1


title: 11w_minus_3


title: 11y_minus_1

source_name: Cultured organoid from pediatric stomach tissue (age 11 year)


title: 11y_minus_3


title: 20w_plus_3


title: 11w_minus_2


title: 11y_minus_2


title: 20w_plus_2


title: 11w_minus_1


title: 11w_plus_2


title: 11y_plus_3


title: 11w_plus_3


title: 11y_plus_2


title: 11y_plus_1


title: Lateral amygdala, Pool 11 (S21_28_33_34), input, ChIPseq

status: Public on Sep 22 2020

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

description: X-linked ChIPseq

data_processing:
RNAseq:  Fastq files were generated from BAM files, and data aligned using TopHat
WGBS:  Alignment was conducted using BWA, and methylation calling  using Samtools
ChIPseq:  Trimming and alignment were conducted using Trimmomatic and BWA
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq:  the "raw.counts" file contains counts gennerated using HTSeq-counts
Supplementary_files_format_and_content: ChIP-Seq:  the "bw" files were generated using deepTools
Supplementary_files_format_and_content: WGBS:  the "profile" files correspond to results from the methylation calling using Samtools

source_name: Brain

extract_protocol: automated protocol, Kapa HTP Lib. Prep. Kit (Illumina)

tag: group

value: Early-Life Adversity group

value: Lateral Amygdala (human brain tissue)


title: Lateral amygdala, Pool 11 (S21_28_33_34), H3K4me3, ChIPseq

description: X-linked ChIPseq

value: H3K4me3:Cell Signaling Technologies, cat #9751BF, lot#6


title: Lateral amygdala, Pool 11 (S21_28_33_34), H3K36me3, ChIPseq

description: X-linked ChIPseq

value: H3K36me3:Active motif, cat #MABI0333, lot #12003


title: Lateral amygdala, Pool 11 (S21_28_33_34), H3K27me3, ChIPseq

description: X-linked ChIPseq

value: H3K27me3:Cell Signaling Technologies, cat #9733S, lot #6


title: Lateral amygdala, Pool 11 (S21_28_33_34), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 11 (S21_28_33_34), H3K9me3, ChIPseq

description: X-linked ChIPseq

value: H3K9me3:Abcam, cat #Ab8898, lot #GR93671-1


title: Lateral amygdala, Pool 10 (S11_13_16), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 11 (S21_28_33_34), H3K4me1, ChIPseq

description: X-linked ChIPseq

value: H3K4me1:Cell Signaling Technologies, cat #5326BF, lot #2


title: 20w_minus_3


title: Lateral amygdala, Pool 10 (S11_13_16), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 10 (S11_13_16), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 10 (S11_13_16), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 10 (S11_13_16), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 10 (S11_13_16), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 7 (S8_30_31_35), H3K36me3, ChIPseq

description: X-linked ChIPseq

value: Control group


title: Lateral amygdala, Pool 7 (S8_30_31_35), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 7 (S8_30_31_35), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 7 (S8_30_31_35), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 7 (S8_30_31_35), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 7 (S8_30_31_35), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 10 (S11_13_16), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 6 (S3_12_38), input, ChIPseq

description: X-linked ChIPseq


title: pfd4_mock_A

status: Public on Dec 22 2020

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

data_processing:
read trimming with cutadapt
read mapping to TAIR10 with HISAT2
read counting with htseq-count
differential expression analysis with DESeq2
Genome_build: TAIR10 (Araport11 anotation)
Supplementary_files_format_and_content: Excel and tab-separated text files with differentially expressed genes and their corresponding statistics (log2FoldChange, pvalue, padj, etc.)

organism: Arabidopsis thaliana

source_name: pfd4 seedlings under standard conditions

extract_protocol:
QIAGEN rneasy plant mini kit
Truseq stranded mRNA kit (Illumina)

tag: genotype/variation

tag: organ

value: whole seedlings

tag: ecotype

tag: growth conditions

value: in vitro, 14 days, LD, ZT1


title: Lateral amygdala, Pool 6 (S3_12_38), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 7 (S8_30_31_35), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 9 (S2_10), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: 11w_plus_1


title: Lateral amygdala, Pool 6 (S3_12_38), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 6 (S3_12_38), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 8 (S14_17_19_23), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 6 (S3_12_38), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 6 (S3_12_38), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 3 (S9_27_39), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: H3K36me3_4h_r3

description:
processed data file: mod_enrichment_rel_to_downstream.txt
processed data file: H3K36me3_4h_ab_R3_diffbind_narrow_FE.bw

source_name: SPO 4h

tag: strain

value: diploid

value: meiotic prophase (4h in SPO)


title: Lateral amygdala, Pool 3 (S9_27_39), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 3 (S9_27_39), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 3 (S9_27_39), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 3 (S9_27_39), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 6 (S3_12_38), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 2 (S1_25), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 2 (S1_25), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 2 (S1_25), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 2 (S1_25), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 2 (S1_25), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 2 (S1_25), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 4 (S6_7), H3K9me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 3 (S9_27_39), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 3 (S9_27_39), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 5 (S22_29_32_37), input, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), H3K36me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), H3K4me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, S38, RNAseq

description:
ribosomal depletion RNA-seq
LatAmy_Brain_RNASeq.raw.counts

extract_protocol: TrueSeq Stranded Total RNA Sample Preparation + Ribo-Zero Gold kits (Illumina)


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), H3K4me1, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), H3K27ac, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, S37, RNAseq


title: Lateral amygdala, S35, RNAseq


title: Lateral amygdala, S36, RNAseq


title: Lateral amygdala, S34, RNAseq


title: Lateral amygdala, S33, RNAseq


title: Lateral amygdala, S31, RNAseq


title: Lateral amygdala, S30, RNAseq


title: Lateral amygdala, S29, RNAseq


title: Lateral amygdala, S32, RNAseq


title: Lateral amygdala, S26, RNAseq


title: Lateral amygdala, S25, RNAseq


title: Lateral amygdala, S27, RNAseq


title: Lateral amygdala, S28, RNAseq


title: Lateral amygdala, S21, RNAseq


title: Lateral amygdala, S20, RNAseq


title: Lateral amygdala, S19, RNAseq


title: Lateral amygdala, S22, RNAseq


title: Lateral amygdala, S17, RNAseq


title: Lateral amygdala, Pool 1 (S4_5_15_20_26_36), H3K27me3, ChIPseq

description: X-linked ChIPseq


title: Lateral amygdala, S16, RNAseq


title: Lateral amygdala, S14, RNAseq


title: Lateral amygdala, S15, RNAseq


title: Lateral amygdala, S13, RNAseq


title: Lateral amygdala, S18, RNAseq


title: Lateral amygdala, S10, RNAseq


title: Lateral amygdala, S11, RNAseq


title: Lateral amygdala, S9, RNAseq


title: Lateral amygdala, S7, RNAseq


title: Lateral amygdala, S6, RNAseq


title: Lateral amygdala, S4, RNAseq


title: Lateral amygdala, S3, RNAseq


title: Lateral amygdala, S8, RNAseq


title: Lateral amygdala, S12, RNAseq


title: Lateral amygdala, S1, RNAseq


title: Lateral amygdala, S2, RNAseq


title: Lateral amygdala, S23, RNAseq


title: Lateral amygdala, S24, RNAseq


title: Lateral amygdala, S38, WGBS

description: Whole Genome Bisulfite Sequencing (WGBS)

extract_protocol: KAPA High Throughput LibraryPreparation Kit (KAPA Biosystems)


title: Lateral amygdala, S36, WGBS


title: Lateral amygdala, S37, WGBS


title: Lateral amygdala, S34, WGBS


title: Lateral amygdala, S35, WGBS


title: Lateral amygdala, S32, WGBS


title: Lateral amygdala, S31, WGBS


title: Lateral amygdala, S28, WGBS


title: Lateral amygdala, S29, WGBS


title: Lateral amygdala, S27, WGBS


title: Lateral amygdala, S26, WGBS


title: Lateral amygdala, S5, RNAseq


title: Lateral amygdala, S22, WGBS


title: Lateral amygdala, S21, WGBS


title: Lateral amygdala, S18, WGBS


title: Lateral amygdala, S19, WGBS


title: Lateral amygdala, S17, WGBS


title: Lateral amygdala, S20, WGBS


title: Lateral amygdala, S14, WGBS


title: Lateral amygdala, S15, WGBS


title: Lateral amygdala, S12, WGBS


title: Lateral amygdala, S13, WGBS


title: Lateral amygdala, S33, WGBS


title: Lateral amygdala, S30, WGBS


title: Lateral amygdala, S11, WGBS


title: Lateral amygdala, S10, WGBS


title: Lateral amygdala, S9, WGBS


title: Lateral amygdala, S6, WGBS


title: Lateral amygdala, S4, WGBS


title: Lateral amygdala, S7, WGBS


title: Lateral amygdala, S8, WGBS


title: Lateral amygdala, S3, WGBS


title: Lateral amygdala, S5, WGBS


title: Lateral amygdala, S2, WGBS


title: Lateral amygdala, S25, WGBS


title: PBAT_EpiLC_dCD

status: Public on Jul 27 2020

first: Alvaro

last: Rada-Iglesias

address: Albert Einstein 22, PCTCAN

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

data_processing:
Genome-wide DNA methylation data was analysed with Bismark (Krueger and Andrews 2011). Briefly, adapter trimming was performed with Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with trim_galore --clip_R1 6 —clip_R2 6 --paired. The resulting reads were mapped with Bismark-v0.16.1 (Krueger and Andrews 2011) and bowtie2-2.2.9 (Langmead and Salzberg 2012), using the “-pbat” setting. Additionally the unmapped reads were remapped as single-end reads and the CpG methylation levels were estimated with the Bismark methylation extractor. Finally only CpGs with a coverage of 3 - 100 reads were considered.
Genome_build: mm10
Supplementary_files_format_and_content: CpG methylation coverage

source_name: epiblast like cells

growth_protocol: ESC were cultured on gelatin-coated plates using Knock-out DMEM supplemented with 15% FBS and LIF. Before each PGCLC differentiation, ESC were adapted to 2i+LIF media (serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 [0.4 μM], GSK3β inhibitor CHIR99021 [3 μM], and LIF) for at least four days in gelatin-coated tissue culture plates. For the EpiLC differentiation, 6-well plates were coated with 15 µg ml-1 Fibronectin and 2 x 105 2i ESC were differentiated in N2B27 media supplemented with 20 ng ml-1 Activin A, 12 ng ml-1 bFGF and 10 µl ml-1 KSR for two days.

extract_protocol:
Bisulfite sequencing libraries were prepared from column-purified DNA of d2 EpiLC using the PBAT method previously described in (Smallwood et al., 2014). Briefly, for the bisulfite conversion the instructions of the EZ Methylation Direct MagPrep Kit (Zymo) were followed.
After purification, bisulfite converted DNAs were eluted from MagBeads directly into 39 µl of first strand synthesis reaction mastermix (1x Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 µM 6NF preamp oligo (IDT)), heated to 65 °C for 3 minutes and cooled on ice. 50 U of klenow exo- (Enzymatics) was added and the mixture incubated on a thermocycler at 37 °C for 30 minutes after slowly ramping from 4 °C. Reactions were diluted to 100 ml and 20 U of exonuclease I (NEB) added and incubated at 37 °C before purification using a 0.8:1 ratio of AMPure XP beads. Purified products were resuspended in 50 ml of second strand mastermix (1x Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 µM 6NR adaptor 2 oligo (IDT) then heated to 98 °C for 2 minutes and cooled on ice. 50 U of klenow exo- (Enzymatics) was added and the mixture incubated on a thermocycler at 37 °C for 90 minutes after slowly ramping from 4 °C. Second strand products were purified using a 0.8:1 ratio of AMPure XP beads and resuspended in 50 ml of PCR mastermix (1x KAPA HiFi Readymix, 0.2 µM PE1.0 primer, 0.2 µM iTAG index primer) and amplified with 12 cycles. The final libraries were purified using a 0.8:1 volumetric ratio of AMPure XP beads before pooling and sequencing. All libraries were prepared in parallel with the pre-PCR purification steps carried out using a Bravo Workstation pipetting robot (Agilent Technologies).

tag: cell line

value: d2 EpiLC

value: Mll3/4 dCD


title: Lateral amygdala, S24, WGBS


title: Lateral amygdala, S23, WGBS


title: Lateral amygdala, S1, WGBS


title: PBAT_EpiLC_Otx2

value: Otx2 KO


title: Lateral amygdala, S16, WGBS


title: RNA_EpiSC_WT_rep2

data_processing:
RNA-seq data generated in R1 WT and dCD cells were analyzed from three replicates for R1 WT and the dCD ESC previously generated by Dorighi et al., 2017, two replicates for R1 WT and dCD d2 EpiLC and two replicates for R1 WT and dCD EpiSC. The transcript abundance was determined with the bootstrap mode of kallisto (-b 100) and the differential expression analyses were performed with sleuth on the gene-level.
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: epiblast stem cells

growth_protocol: ESC were cultured on gelatin-coated plates using Knock-out DMEM supplemented with 15% FBS and LIF. Before each PGCLC differentiation, ESC were adapted to 2i+LIF media (serum-free N2B27 medium supplemented with MEK inhibitor PD0325901 [0.4 μM], GSK3β inhibitor CHIR99021 [3 μM], and LIF) for at least four days in gelatin-coated tissue culture plates. For the EpiLC differentiation, 6-well plates were coated with 15 µg ml-1 Fibronectin and 2 x 105 2i ESC were differentiated in N2B27 media supplemented with 20 ng ml-1 Activin A, 12 ng ml-1 bFGF and 10 µl ml-1 KSR for two days. For EpiSC differentiation, 2i ESC were plated at a density of 2.5 x 105 cells ml-1 on plates coated with 15 µg ml-1 Fibronectin and differentiated into EpiSC by passaging them in N2B27 media supplemented with 20 ng ml-1 Activin A and 12 ng ml-1 bFGF for at least eight days. For the PGCLC differentiation, d2 EpiLC were plated at a density of 2 x 104 cells ml-1 and cultured as embryoid bodies (EB) on Ultra-Low attachment multiwell plates (Corning® Costar®) in GK15 medium supplemented with growth factors (0.5 µg ml-1 BMP4, 0.1 µg ml-1 SCF, 1000 U ml-1 LIF and 50 ng ml-1 EGF, no BMP8a) for four days.

extract_protocol:
RNA from ESC, EpiLC and EpiSC was extracted following the protocol of the innuPREP DNA/RNA mini kit (Analytik Jena), while for the RNA extraction from d2 EB, d4 EB and sorted PGCLC the ReliaPrep™ RNA Miniprep Systems (Promega) was used.
Illumina TruSeq stranded

value: EpiSC

value: wild type


title: RNA_EpiSC_WT_rep1


title: RNA_EpiSC_dCD_rep2


title: RNA_EpILC_dCD_rep2


title: RNA_EpiSC_dCD_rep1


title: RNA_EpiLC_WT_rep2


title: EXP1030RNA12

city: Tampa

first: Marco

last: Davila

state: FL

address: 12902 Usf Magnolia Dr

department: BMT-CI

institute: Moffitt Cancer Center and Research Institute

data_processing:
Illumina NextSeq 500 pair-end reads from RNA-Seq libraries were first adaptor trimmed
STAR v2.5.3a was used for alignment to the reference genome.
HTSeq v0.6.1 was used for reads counting to estimate expression level of genes
Library size normalization was performed using DESeq2
Genome_build: GRCh37
Supplementary_files_format_and_content: comma-delimited text file including read counts of each gene (in rows) for each sample (in columns)

source_name: Lymphoma tumor biopsy

extract_protocol:
Total RNA was extracted using the Allprep Qiagen Kit according to the manufacturer’s instructions
Total RNA-seq libraries were generated from 100 ng of RNA using the Nugen Ovation Human FFPE RNA-Seq kit according to the manufacturer’s instructions

value: Low

tag: response

value: Insufficient Followup


title: EXP1030RNA11

value: High

value: NDR


title: RNA_EpiLC_WT_rep1


title: EXP1030RNA10


title: EXP1030RNA9


title: EXP1030RNA8


title: EXP1030RNA4


title: EXP1030RNA6


title: EXP1030RNA5


title: EXP1030RNA3


title: EXP1030RNA2


title: EXP964RNA13

value: DR


title: EXP900RNA2


title: EXP900RNA1


title: EXP964RNA7


title: EXP964RNA8


title: EXP964RNA6


title: EXP925RNA12


title: EXP964RNA2


title: EXP964RNA5


title: EXP925RNA9


title: RNA_EpILC_dCD_rep1


title: EXP925RNA8


title: EXP925RNA4


title: EXP900RNA7


title: EXP900RNA6


title: 20190716_JainIO360Cart2_06S19065875_09

type: RNA

hyb_protocol: Hybridization of biotinylated reporter probes was carried out according to the manufacturer's protocol

scan_protocol: Scanning was perfomred on the nCounter Digital Analyzer at 550 FOV

data_processing: Nanostring nSolver was used for processing data and normalization

label: biotin

extract_protocol: Retrospective FFPE or prospective snap frozen tumor samples were evaluated for tumor content by a pathologist. DNA and RNA were extracted using the Allprep Qiagen Kit according to the manufacturer’s instructions

tag: neurotoxicity


title: 20190716_JainIO360Cart2_06S19065871_05

label_protocol: Hybridization of biotinylated reporter probes was carried out according to the manufacturer's protocol


title: 20190716_JainIO360Cart2_06S19065874_08


title: 20190716_JainIO360Cart2_06S19065872_06


title: 20190716_JainIO360Cart2_06S19065870_04


title: 20190206_JainIO360Cart1_EXP964RNA7-06S19010312_06


title: 20190206_JainIO360Cart1_EXP964RNA12-06S19010317_10


title: 20190206_JainIO360Cart1_EXP964RNA2-06S19010307_02


title: 20190206_JainIO360Cart1_EXP964RNA13-06S19010318_11


title: 20181127_Cart02_EXP925RNA6_05


title: 20190206_JainIO360Cart1_EXP964RNA3-06S19010309_03


title: 20190206_JainIO360Cart1_EXP964RNA6-06S19010311_05


title: 20190206_JainIO360Cart1_EXP964RNA11-06S19010316_09


title: 20181127_Cart02_EXP925RNA9_08


title: 20181127_Cart02_EXP925RNA8_07


title: EXP925RNA5


title: 20181127_Cart02_EXP925RNA11_10


title: 20180831_CART1-FOV555_EXP892RNA5_04


title: 20181127_Cart02_EXP925RNA2_02


title: 20180831_CART1-FOV555_EXP900RNA1_05


title: 20180831_CART1-FOV555_EXP900RNA6_10


title: 20181127_Cart02_EXP925RNA1_01


title: 20181127_Cart02_EXP925RNA5_04


title: 20190716_JainIO360Cart2_06S19065877_11


title: 20180831_CART1-FOV555_EXP892RNA1_01


title: 20190716_JainIO360Cart2_06S19065876_10


title: 20190716_JainIO360Cart2_06S19065873_07


title: 20180831_CART1-FOV555_EXP892RNA4_03


title: 20190716_JainIO360Cart2_06S19065869_03


title: 20190206_JainIO360Cart1_EXP964RNA8-06S19010313_07


title: 20181127_Cart02_EXP925RNA4_03


title: 20190206_JainIO360Cart1_EXP964RNA5-06S19010310_04


title: 20181127_Cart02_EXP925RNA12_11


title: Water treatment_rep3

status: Public on Jul 04 2020

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

country: China

institute: Yangzhou University

description:
The transcriptome of Streptococcus suis following treatment with water
Nor3

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Streptococcus suis SC84, complete genome (NC_012924.1).
Supplementary_files_format_and_content: read counts for each gene and each sample.
Supplementary_files_format_and_content: fpkm values for each gene and each sample.

organism: Streptococcus suis

source_name: H2O-treated Streptococcus suis

growth_protocol: Streptococcus suis was grown at 37 °C in Tryptic Soy Broth (TSB) supplemented with 10% (vol/vol) newborn bovine serum.  Overnight culture of the strain was diluted 1:100 in fresh medium, and grown to the mid-exponential phase (OD600 = 0.6).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The culture was divided into 3 aliquots, which were supplemented with 2 mM FeSO4, 0.25 mM CoSO4, or H2O, respectively. Following 15 min treatment, bacterial cells were collected for RNA extration.

tag: treatment

value: H2O (control),15 min

tag: growth phase

value: mid-exponential phase


title: Water treatment_rep1

description:
The transcriptome of Streptococcus suis following treatment with water
Nor1


title: 20180831_CART1-FOV555_EXP900RNA7_11


title: WT_Y1P_WCE_rep2 [144_Y1]

status: Public on Jun 30 2020

city: Oxford

first: Dong-hyuk

last: Heo

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Adaptor and low quality sequence were removed by Trimmomatic v0.39
Reads were aligned to the concatenated genome (S. pombe + S. cerevisiae) by Bowtie2 v2.3.5.1
Uniquely mapped reads were separated based on species by Samtools v1.9
The alignment files  were converted to bedgraph format by Bedtools v2.26.0
Genome_build: S. pombe genome version ASM294v2.28
Supplementary_files_format_and_content: bigWig

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe strains were grown in YES media(0.5% yeast extract, 3% glucose, 0.0225% supplements (Histidine, Adenine, Uracil, Leucine, Lysine) to exponential phase at 30°C. Meantime S. cerevisiae cells were grown YPD(1% yeast extract, 2% peptone, and 2% glucose). S. cerevisiae cells correspond to 10% of S. pombe cells were added to S. pombe cells.

extract_protocol:
Cells were crosslinked using 11% formaldehyde and lysed by vortexing with glass beads. The chromatin was sheared by sonication and extracted by ultra-centrifugation steps.
NEBNext Fast DNA Library Prep Set for Ion Torrent kit

tag: strain background

value: Wild-type


title: 20180831_CART1-FOV555_EXP892RNA2_02


title: ssu72_Y1P_WCE_rep2 [700_Y1]

value: ssu72 deletion


title: ssu72_Y1P_IP_rep2 [700_Y1]

tag: chip antibody

value: Tyr1 (Y1, clone:3D12 monoclonal, Active Motif, cat No.:61384)


title: WT_Y1P_IP_rep2 [144_Y1]


title: WT_S2P_WCE_rep2 [144_S2]


title: ssu72_S2P_WCE_rep2 [700_S2]


title: Water treatment_rep2

description:
The transcriptome of Streptococcus suis following treatment with water
Nor2


title: ssu72_S2P_IP_rep2 [700_S2]

value: Ser2 (S2, clone:3E10 monoclonal, Millipore, cat No.:04-1571)


title: WT_S2P_IP_rep2 [144_S2]


title: ssu72_Rpb1_IP_rep2 [700_8WG16]

value: Rpb1 (clone:8WG16 monoclonal, Millipore, cat No.:05-952)


title: Lateral amygdala, Pool 2 (S1_25), H3K27me3, ChIPseq

description: X-linked ChIPseq

value: Early-Life Adversity group

tag: tissue

value: Lateral Amygdala (human brain tissue)

value: H3K27me3:Cell Signaling Technologies, cat #9733S, lot #6


title: ssu72_Rpb1_WCE_rep2 [700_8WG16]


title: WT_Rpb1_IP_rep2 [144_8WG16]


title: WT_Y1P_WCE_rep1 [144_Y1]


title: 20190716_JainIO360Cart2_06S19065868_02


title: ssu72_Y1P_IP_rep1 [700_Y1]


title: WT_Rpb1_WCE_rep2 [144_8WG16]


title: 20180831_CART1-FOV555_EXP900RNA2_06


title: E423P-mitoRNA

status: Public on Jul 14 2020

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

description:
Total mitochodnrial RNA
S2_E423P-mitoRNA

data_processing:
QC performed usinf fastQC
Trmming applied using Cutadapt
Alignment performed using Bowtie2
samtools stats used to calculated mismatches and error rates
bcftools view and vcfutils.pl varFilter was used to generate dinucleotide transitions and transversions
Genome_build: Drosophila melanogster (DM6)
Supplementary_files_format_and_content: Tab delimited Gene Counts

molecule: other

organism: Drosophila melanogaster

source_name: E423P mitochondria

extract_protocol:
Whole adult fly mitochondria were extracted and mitochondrial RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total mitochodnrial RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: E423P RNA polymerase overexpression

tag: age

value: Two weeks old


title: WT-mitoRNA

description:
Total mitochondrial RNA
S1_WT-mitoRNA

source_name: Wild type mitochondria

value: Wild type RNA polymerase overexpression


title: ssu72_S2P_WCE_rep1 [700_S2]


title: WT_S2P_WCE_rep1 [144_S2]


title: WT_Y1P_IP_rep1 [144_Y1]


title: WT_S2P_IP_rep1 [144_S2]


title: ssu72_S2P_IP_rep1 [700_S2]


title: ssu72_Rpb1_WCE_rep1 [700_8WG16]


title: WT_Rpb1_WCE_rep1 [144_8WG16]


title: ssu72_Rpb1_IP_rep1 [700_8WG16]


title: ssu72_S7P_IP

data_processing:
Adaptor and low quality sequence were removed by Trimmomatic v0.39
Reads were aligned to the concatenated genome (S. pombe + S. cerevisiae) by Bowtie2 v2.3.5.1
Uniquely mapped reads were separated based on species by Samtools v1.9
The alignment files  were converted to bigwig format by Bedtools v2.26.0
Genome_build: S. pombe genome version ASM294v2.28
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cells were crosslinked using 11% formaldehyde and lysed by vortexing with glass beads. The chromatin was sheared by sonication and extracted by ultra-centrifugation steps.
NEBNext Ultra DNA Library Prep Kit for Illumina

value: Ser7 (S7, clone:4E12 monoclonal, Millipore, cat No.:04-1570)


title: ssu72_S5P_WCE_rep2


title: WT_S7P_IP


title: WT_S5P_WCE_rep2


title: WT_S7P_WCE


title: WT_Rpb1_IP_rep1 [144_8WG16]


title: hos2Δssu72Δ rep1 [DH-16]

data_processing:
The libraries were sequenced by Illumina NextSeq 500.
Adaptor and low quality sequence were removed by Trimmomatic v0.39
Reads were aligned to the concatenated genome (S. pombe + S. cerevisiae) by Bowtie2 v2.3.5.1
Uniquely mapped reads were separated based on species by Samtools v1.9
Uniquely mapped to S. pombe reads were separated based on the strand by Samtools v1.9
The alignment files  were converted to bedgraph format by Bedtools v2.26.0
Genome_build: ASM294v2.25 from pombase.org
Supplementary_files_format_and_content: bedgraph

growth_protocol: S. pombe strains were grown in YES media(0.5% yeast extract, 3% glucose, 0.0225% supplements (Histidine, Adenine, Uracil, Leucine, Lysine) to exponential phase at 30°C. Meantime S. cerevisiae cells were grown YPD (1% yeast extract, 2% peptone, and 2% glucose). S. cerevisiae cells correspond to 10% of S. pombe cells were added to S. pombe cells.

extract_protocol:
Total RNAs were extracted by a standard hot phenol method.
NEBNext ultra II directional RNA library prep kit for Illumina

value: hos2 and ssu72 deletion


title: WT_S5P_IP_rep1

value: Ser5 (S5, clone:3E8 monoclonal, Millipore, cat No.:04-1572)


title: WT_S5P_IP_rep2


title: ssu72_Y1P_WCE_rep1 [700_Y1]


title: ssu72_S7P_WCE


title: ssu72_S5P_WCE_rep1


title: WT_S5P_WCE_rep1


title: Sample 16_leaf_Col0_Rep3.sRNA-seq

status: Public on Jun 25 2020

city: Vienna

first: Ranjith

last: Papareddy

address: Dr Bohr Gasse 3

country: Austria

institute: Gregor Mendel Institute

description:
Single-end 50 base read small RNA seq data from leaf_Col0 from replicate 3
leaf_Col0_Rep3.sRNA-seq

data_processing:
Small RNA-seq Analysis: Adaptor trimming with Cutadapt parameters "cutadapt -a AGATCGGAAGA  -m 18 -M 30 --trimmed-only". End to End alignment with zero mismatched and upto 100 multimappers  against TAIR10  Arabidopsis thaliana genome with STAR "STAR --outFilterMultimapNmax 100 --outSAMtype SAM --outFilterMismatchNmax 0 --alignEndsType EndToEnd --outReadsUnmapped Fastx --alignIntronMax 1 --outSAMprimaryFlag AllBestScore".  Multi mapping reads rescued with rich-get-richer algorithem " readmapIO.py  ". Resulting bedfiles sorted, collapsed and normalized to totoal genome matching reads.
MethylC-Seq Analysis: Adaptor trimming with  trimeGalore (a wraper up trimmerer from Cutadapt) along with quality trimming, 6nt from 3' and 5' end were remove to exclude random hexamers used in preamplification step of methylome library preperation. After quality filtering and adaptor trimming, bisulfite-converted reads were aligned against the TAIR10 genome  using Bismark (bismark --non_directional -q --score-min L,0,-0.4) and deduplicated with function deduplicate_bismark -s --bam. Aligned BAM files with unique mapping reads and clonal deduplated were used as  input for the Methylpy software (https://bitbucket.org/schultzmattd/methylpy) to extract weighted methylation rate at each covered Cytosine site. Bisulfite conversion rates were calculated using the unmethylated chloroplast genome or spiked-in unmethylated Lambda phage DNA controls (European Nucleotide Archive Accession Number J02459, Promega catalog number D1521)
Genome_build: TAIR10
Supplementary_files_format_and_content: sRNA-Seq: Bed files contain tab-separated values of chromosomes (column 1), start (column 2) and stop (column 3) coordinates of smallRNAs followed by normalize RPM score (column 4), strand (column 5), sequence (column 6) and small RNA size (column 7)
Supplementary_files_format_and_content: MethylC-seq:  All Cytosin containing tab-separated values of chromosomes (column 1), start position(column 2)  of cytosine followed by strand  (column 3), Trinucleotide context  (column 4), count of reads supporting methylation (column 5) and total reads  (column 6); In addition ,Bigwig files containing chromosomes (column 1), start (column 2) and stop (column 3) and weighted methylation rate (column 4)

growth_protocol: Controlled growth chamber at 20˚C-22˚C with a 16-h light/8-h dark cycle. Plants were four weeks old when tissue was harvested.

extract_protocol:
samples 1 to 28 : Total RNA extracted with TRIzol reagent (Thermo Fisher Scientific) and size selected for 18-30nt RNA molecules with denaturing urea gel; Samples 29 to 69 : genomic DNA extracted with Quick-DNATM Micro prep Kit (Zymo D3020)
Samples 1 to 28 : Size selected RNA was used to synthesise cDNA with NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (cat. no E7300; New England Biolabs) according to the manufacturer’s recommendations. Various numbers of PCR cycles were used to amplify cDNAs: 18, 20, 22, and 24 PCR cycles for globular; 14, 16, 18, and 20 PCR cycles for early heart and 3 weeks old leaf samples. Final PCR amplicons were initially run on a 90% (v/v) formamide/8% (w/v) acrylamide gel for 30 min at 5W, followed by 30W for ≥2 h, and stained with SYBR Gold (1:10,000; Thermo Fisher Scientific). Intensity of PCR amplicons between 137-bp and 147-bp  Fluorescence intensities of amplicons were examined across the PCR cycles, 137-bp to 149-bp corresponding to 18- nucleotide to 30- nucleotide sRNAs with adapters respectively was inspected under UV transilluminator. Amplicons with  non-saturated signals from PCR cycles were gel-purified. Gel purified small RNA libraries are resuspenden in 15 μL of Elution Buffer (Qiagen). Finally small RNA libraries quality checked for expected size range with Agilent High sensitivity NGS fragment Kit (DNF-474-1000) were sequenced on a HiSeq 2500 instrument (Illumina) in 50 base single-end mode.
Samples 29 to 69 : Genomic DNA subjected to genomic DNA  bisulfite treatment for 200 minutes with EZ DNA Methylation-DirectTM Kit (Zymo D5020).preamplified for two cycles with primers (5′-CCCTACACGACGCTCTTCCGATCTNNNNNN-3′) containing random hexamers and purified using the Zymo DNA Clean and Concentrator kit. Adaptor primers (5′-CAGACGTGTGCTCTTCCGATCTNNNNNN-3′) were added to preamplified products and then amplified for 12 PCR cycles with indexing primers for Illumina sequencing. Methylome libraries were purified using Beckman Coulter AMPureXP DNA beads.
samples 1 to 28 : smallRNA-seq; samples 29 to 69: MethylC-Seq

tag: genotype acronym

value: wild type

value: 3-weeks old leaf

tag: treatment nucleic acids prior to library construction

tag: amount of total rna used for library construction


title: WT rep1 [WTCHG_337412_285159]

source_name: WT

growth_protocol: S. pombe strains were grown in YES media(0.5% yeast extract, 3% glucose, 0.0225% supplements (Histidine, Adenine, Uracil, Leucin, Lysine) to exponential phase at 30°C. Meantime S. cerevisiae cells were grown YPD(1% yeast extract, 2% peptone, and 2% glucose). S. cerevisiae cells correspond to 10% of S. pombe cells were added to S. pombe cells.


title: ssu72_S5P_IP_rep2


title: RNA-seq, HaCaT Keratinocyte cells, unstimulated rep4

status: Public on May 27 2020

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

institute: the university of manchester

description: 7 replicates of RNA-seq for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours

data_processing:
The sequencing data was filtered and adapters were removed using fastp v0.19.4 (S. Chen et al., 2018). The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0 (Servant et al., 2015), using default settings. The Hi-C interaction matrices were normalised within Hi-C Pro using iterative correction and eigenvector decomposition (ICE). TADs were identified using OnTAD v1.2 (An et al., 2019), a novel Optimized Nested TAD caller for Hi-C data, using Hi-C data binned at a 40 kb resolution and a maximum TAD size of 4 mb. Files for visualisation were created using the hicpro2juicebox.sh utility and visualised in Juicebox (Durand et al., 2016).
Sequencing data for the HiChIP libraries was filtered and the adapters were removed using fastp v0.19.4 (S. Chen, Zhou, Chen, & Gu, 2018). The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0 (Servant et al., 2015), using default settings. Enriched regions (H3K27ac peaks) were identified using HiChIP-peaks v 0.1.1 (Shi, Rattray, & Orozco, 2019) with default settings and FDR < 0.01. Loops were identified using FitHiChIP (Bhattacharyya, Chandra, Vijayanand, & Ay, 2019) using the following settings: Coverage normalization, stringent background with merging enabled, peaks generated from HiChIP-peaks and 5 kb bin size.
RNA-seq: Reads were quality trimmed using Trimmomatic v0.38 using a sliding window of 5 with a mean minimum quality of 20. Adapters and poly A/poly G tails were removed using Cutadapt v1.18 and then UMIs were extracted from the 5’ of the reads using UMI-tools v0.5.5. Reads were then mapped using STAR v2.5.3a on the GRCh38 genome with GENCODE annotation v29. Reads were de-duplicated using UMIs with UMI-tools and then counted using HTSeq v0.11.2. Count matrixes were analysed in R 3.5.1 and normalisation and differential expression analysis was conducted using DESeq2 v1.22.2.
Genome_build: hg38
Supplementary_files_format_and_content:
HiC/*.hic files: Hi-C files for juicebox
HiC/OnTAD*.bed.gz: TAD calls from OnTAD
HiChIP/*WashU.bed.gz: washu files containing significant interactions from FitHiChIP
HiChIP/*peaks.bed peak calls from HiChIP-peaks
HiChIP/*bedgraph.bdg HiChIP enrichment signal from HiChIP-peaks
RNA/DEgenes_HAC_STvsUNST.csv: DESeq2 results from contrast HaCaT stimulated vs unstimulated
RNA/hacat_myla_norm_counts.csv: Normalized counts from DESeq2 with all samples

source_name: HaCaT Keratinocyte cells

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) and RNA integrity was assessed using the Bioanalyzer Agilent RNA 6000 Nano Kit (Agilent Technologies).
Sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

value: HaCaT Keratinocyte cell line

tag: stimulation

tag: restriction enzyme


title: RNA-seq, GM12878 cells rep1

description: 2 replicates of RNA-seq for GM12878 cells

source_name: GM12878 cells

growth_protocol: GM12878 cells were cultured in RPMI 1640 with 2mM L glutamine media supplemented with 15% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) and RNA integrity was assessed using the Bioanalyzer Agilent RNA 6000 Nano Kit (Agilent Technologies).
Sequencing library was generated using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

value: GM12878 cells


title: RNA-seq, My-La CD8+ T lymphocyte cells

description: 1 replicate of RNA-seq for MyLa CD8+ T cells

source_name: My-La CD8+ T lymphocyte cells

growth_protocol: My-La cells were cultured in RPMI 1640 medium supplemented with 10% AB human serum, 100 U/mL recombinant human IL-2 and 1% penicillin-streptomycin in 25cm2 vented culture flasks at 37C/5% CO2

value: My-La CD8+ T lymphocyte cell line


title: RNA-seq, HaCaT Keratinocyte cells, unstimulated rep3

description: 6 replicates of RNA-seq for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours


title: RNA-seq, GM12878 cells rep2

description: 3 replicates of RNA-seq for GM12878 cells


title: RNA-seq, HaCaT Keratinocyte cells, stimulated rep3

description: 3 replicates of RNA-seq for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours

growth_protocol: HaCaT cells were cultured in high glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 75cm2 vented culture flasks at 37C/5% CO2. Cells were stimulated with 100 ng/mL recombinant human IFN-γ (285-IF-100; R&D Systems) for 8 hours.

value: 100 ng/mL recombinant human IFN-γ for 8 hours


title: RNA-seq, HaCaT Keratinocyte cells, stimulated rep1


title: RNA-seq, HaCaT Keratinocyte cells, unstimulated rep2

description: 5 replicates of RNA-seq for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours


title: RNA-seq, HaCaT Keratinocyte cells, unstimulated rep1

description: 4 replicates of RNA-seq for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours


title: RNA-seq, HaCaT Keratinocyte cells, stimulated rep2


title: E3

status: Public on Jun 23 2020

city: Chengdu

first: Ling

last: xu

state: Sichuan

address: No. 211 Huimin road

department: College of animal science and technology

institute: Sichuan Agricultural University

data_processing:
Clean Reads was sequenced to the reference genome using TopHat2
The Mapped notes were pieced together using Cufflinks software and compared with the original genome annotation information to search for previously unannotated transcriptional areas and to excavate new transcripts and new genes of the species to complement and refine the original genome annotation information.
Cuffquant and Cuffnorm used FPKM (Fragments Per Kilobase of transcript Per Million Fragments mapped) as an indicator to measure transcription or gene expression level.
The set of genes obtained by differential expression analysis is called differential expression gene set and is named "A_vs_B".Differentially expressed genes can be classified into up-regulated and down-regulated genes, depending on the relative level of expression between the two samples.
Genome_build: OryCun2.0_NCBI.Oryctolagus_cuniculus
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oryctolagus cuniculus

source_name: rabbit endometrium

extract_protocol:
RNA was harvested using Trizol reagent
A sequencing library was generated using the Illumina kit. The eukaryotic mRNA was enriched with magnetic beads with Oligo (dT); the mRNA was randomly interrupted by the addition of Fragmentation Buffer; the first cDNA strand was synthesized using random hexamers using mRNA as a template, and then The second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I, and the cDNA was purified by AMPure XP beads; the purified double-stranded cDNA was subjected to end repair, A tail was added and the sequencing linker was ligated, and then AMPure XP beads were used. Fragment size selection; finally, a cDNA library was obtained by PCR enrichment. Initial quantification was performed using Qubit2.0, and the insert size of the library was detected using Agilent 2100. After passing the library test, different libraries are merged based on the amount of target data and sequenced using the Illumina HiSeq platform.

value: endometrium

tag: body weight


title: DRIPc_seq_siUAP56_1

status: Public on May 25 2020

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

data_processing:
Library strategy: DRIP-seq
DRIPc-seq, DRIP-seq, ChIP-seq and RNA-seq: All fastq files were trimmed with FASTQ Toolkit before mapping
DRIPc-seq, DRIP-seq and ChIP-seq reads were aligned to the hg 38 Canonical genome using Bowtie2/BWA.
DRIPc-seq and ChIP-seq peaks were called using MACS2 callpeak.
RNA-seq reads were aligned to the hg 38  genome using HISAT2, counted using FeatureCounts and normalized by RPKM.
Bigwig files were generated using bedtools bamcoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Erythromyeloblastoid leukemia cell line

extract_protocol:
Genomic DNA from K562 cells enzimatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.  Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
Standard illumina protocol

tag: antibody

value: Monoclonal S9.6

tag: genotype/variation


title: DRIPc_seq_siC_1

tag: cell line

value: siC control


title: D3 TGFb 5ng/ml-2

status: Public on Apr 24 2020

city: Foster City

first: Ricardo

last: Ramirez

address: 333 Lakeside Drive

institute: Gilead Sciences, Inc.

data_processing:
Basecalls from Illumina samples were performed using CASAVA
Reads were aligned to mouse genome assembly mm10 using STAR 2.4 with the following parameters: --readFilesIn 107_L4.D702_1.clipped.fastq.gz   107_L4.D702_2.clipped.fastq.gz      --readFilesCommand zcat      --outFileNamePrefix 107_L4.D702.   --outSAMstrandField intronMotif   --outSAMattributes NH      --outSAMunmapped Within   --outFilterIntronMotifs RemoveNoncanonicalUnannotated   --alignSJoverhangMin 8   --chimSegmentMin 15   --chimScoreMin 1   --chimScoreDropMax 20   --chimScoreSeparation 10   --chimJunctionOverhangMin 17   --sjdbOverhang 200   --sjdbScore 3   --quantMode TranscriptomeSAM  @CO     user command line: /ea/bin/STAR-2.4 --readFilesIn 107_L4.D702_1.clipped.fastq.gz 107_L4.D702_2.clipped.fastq.gz --genomeDir /ea/indexes/DNA/m_musculus/mm10.fa.derived/eaGene4/star --runThreadN 22 --readFilesCommand zcat --chimSegmentMin 15 --chimJunctionOverhangMin 17 --chimScoreMin 1 --chimScoreDropMax 20 --chimScoreSeparation 10 --quantMode TranscriptomeSAM --outSAMattributes NH --alignSJoverhangMin 8 --sjdbScore 3 --outSAMunmapped Within --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --sjdbOverhang 200
Basecalls from Ion Torrent samples were performed using BaseCaller (Torrent Suite v5.0.1)
Reads were aligned to the hg19 AmpliSeq Transcriptome ERCC using tmap v5.6.8 with the following parameters: mapall -q 50000 -n 12 -f /results/referenceLibrary/tmap-f3/hg19_ampliseq_transcriptome_ercc_v1/hg19_ampliseq_transcriptome_ercc_v1.fasta -i bam -v -Y -u --prefix-exclude 5 -o 2 stage1 map4
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Read counts per gene per sample

source_name: Primary Hepatic Stellate Cells (HSCs)

extract_protocol:
RNA samples were converted into cDNA libraries using the Illumina TruSeq  Stranded mRNA sample preparation kit (Illumina # RS-122-2103).
Libraries were prepared for sequencing using the Ampliseq human transcriptome kit (Thermo) for sequencing on Ion Torrent

tag: cell type

value: Primary Hepatic Stellate Cells (HSCs)

tag: donor

value: Donor 3

tag: culture condition

value: serum free media

value: TGFb 5ng/ml

tag: treatment time

value: 48 hours


title: D3 TGFb 5ng/ml-1

tag: treatment


title: D3 TGFb 5ng/ml + ACCi 300nM-2

value: TGFb 5ng/ml + ACCi 300nM


title: D3 TGFb 5ng/ml + ACCi 300nM-1


title: D3 TGFb 5ng/ml + TGFi 5uM-1

value: TGFb 5ng/ml + TGFi 5uM


title: D3 TGFb 5ng/ml + TGFi 5uM-2


title: D3 DMSO-2

value: DMSO


title: WT rep2 [DH-20]

tag: strain background

value: Wild-type


title: D3 DMSO-1


title: D3 ACCi 300nM-2

value: ACCi 300nM


title: ssu72_S5P_IP_rep1

value: ssu72 deletion

tag: chip antibody

value: Ser5 (S5, clone:3E8 monoclonal, Millipore, cat No.:04-1572)


title: hos2Δssu72Δ rep2 [DH-23]

value: hos2 and ssu72 deletion


title: D3 ACCi 300nM-1


title: D3 TGFi 5uM-1

value: TGFi 5uM


title: ssu72Δ rep1 [DH-14]


title: D2 TGFb 5ng/ml + ACCi 300nM-1

value: Donor 2


title: D2 TGFb 5ng/ml-2


title: D2 TGFb 5ng/ml-1


title: ssu72Δ rep2 [DH-21]


title: D2 TGFb 5ng/ml + TGFi 5uM-1


title: hos2Δ rep2 [DH-22]

value: hos2 deletion


title: D2 TGFb 5ng/ml + TGFi 5uM-2


title: D2 DMSO-2


title: ssu72Δ rep1 [WTCHG_337412_286171]


title: D3 TGFi 5uM-2


title: hos2Δ rep1 [DH-15]


title: WT rep1 [DH-13]


title: D2 ACCi 300nM-2


title: D2 DMSO-1


title: D2 ACCi 300nM-1


title: ssu72Δ rep2 [WTCHG_337412_290124]


title: D2 TGFi 5uM-2


title: D2 TGFb 5ng/ml + ACCi 300nM-2


title: D2 TGFi 5uM-1


title: D1 TGFb 5ng/ml-2

value: Donor 1


title: D1 TGFb 5ng/ml-1

value: Primary Hepatic Stellate Cells (HSCs)


title: D1 TGFb 5ng/ml + ACCi 300nM-2


title: D1 Acci 300nM-1


title: D1 TGFb 5ng/ml + TGFi 5uM-1


title: Sample 14_leaf_Col0_Rep1.sRNA-seq

description:
Single-end 50 base read small RNA seq data from leaf_Col0 from replicate 1
leaf_Col0_Rep1.sRNA-seq

tag: genotype

value: wild type

tag: tissue

value: 3-weeks old leaf

value: 80% of RNA from 50 embryos


title: D1 Acci 300nM-2

value: serum free media

value: 48 hours


title: D1 DMSO-2


title: FFD_ACCi_5mpk_80

source_name: Liver

tag: strain

value: liver

tag: diet

value: fast food diet (FFD)

value: 28 days


title: D1 TGFi 5uM-2


title: D1 TGFi 5uM-1


title: FFD_ACCi_5mpk_77


title: FFD_ACCi_5mpk_78


title: FFD_ACCi_5mpk_73


title: FFD_ACCi_5mpk_76


title: FFD_ACCi_5mpk_74


title: FFD_ACCi_5mpk_71


title: Hi-C, HaCaT Keratinocyte cells, stimulated

description: Hi-C library for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015)
Sequencing libraries were generated with 6-8 cycles of PCR using Truseq single indexes (Illumina) and Phusion polymerase (NEB)

treatment_protocol: Cells were fixed in 1% formaldehyde for 10 minutes at room temperature, Fixation was quenched by the addition of cold 1M glycine to a final concentration of 0.125M. Pelleted cells were frozen on dry ice and stored at -80C.

value: HaCaT Keratinocyte cell line

tag: stimulation

value: 100 ng/mL recombinant human IFN-γ for 8 hours

value: HindIII


title: HiChIP, My-La CD8+ T lymphocyte cells

description: 2 replicates and combined HiChIP libraries for MyLa CD8+ T cells

extract_protocol:
Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed for 30 minutes at 4C with rotation. The nuclei were permeabilised and the chromatin was digested with MboI. Ends were marked with biotin followed by in-nucleus ligation, shearing by sonication and immunoprecipitation with an antibody for H3K27ac (Abcam ab4729). De-crosslinking, biotin pulldown and tagmentation was conducted according to the previously established HiChIP protocol (Mumbach et al., 2016)
Sequencing library was generated with 10 cycles of PCR using Nextera dual index primers and Phusion HF 2X (NEB)

value: My-La CD8+ T lymphocyte cell line

tag: restriction enzyme

value: MboI


title: HiChIP, HaCaT Keratinocyte cells, unstimulated

description: 2 replicates and combined HiChIP libraries for HaCaT keratinocyte cells


title: Hi-C, HaCaT Keratinocyte cells, unstimulated

description: Hi-C library for HaCaT keratinocyte cells


title: D1 TGFb 5ng/ml + ACCi 300nM-1

value: TGFb 5ng/ml + ACCi 300nM


title: D1 TGFb 5ng/ml + TGFi 5uM-2

value: TGFb 5ng/ml + TGFi 5uM


title: Hi-C, My-La CD8+ T lymphocyte cells

description: Hi-C library for MyLa CD8+ T cells

treatment_protocol: Cells were fixed in 2% formaldehyde for 10 minutes at room temperature, Fixation was quenched by the addition of cold 1M glycine to a final concentration of 0.125M. Pelleted cells were frozen on dry ice and stored at -80C.


title: FFD_ACCi_5mpk_70


title: FFD_ACCi_1mpk_67


title: FFD_ACCi_5mpk_68-T


title: HiChIP, HaCaT Keratinocyte cells, stimulated

description: 2 replicates and combined HiChIP libraries for HaCaT keratinocyte cells stimulated with IFN-γ for 8 hours


title: FFD_ACCi_1mpk_66


title: Sample 15_leaf_Col0_Rep2.sRNA-seq

description:
Single-end 50 base read small RNA seq data from leaf_Col0 from replicate 2
leaf_Col0_Rep2.sRNA-seq

tag: genotype acronym

tag: treatment nucleic acids prior to library construction

tag: amount of total rna used for library construction


title: FFD_ACCi_1mpk_59


title: FFD_ACCi_1mpk_64


title: FFD_ACCi_1mpk_61


title: FFD_ACCi_1mpk_65-T


title: FFD_ACCi_1mpk_57


title: FFD_ACCi_1mpk_55


title: FFD_veh_41

value: Vehicle


title: FFD_ACCi_1mpk_58


title: D1 DMSO-1

value: Primary Hepatic Stellate Cells (HSCs)

value: Donor 1

value: DMSO


title: FFD_veh_40


title: FFD_ACCi_5mpk_72-T


title: FFD_veh_35


title: FFD_veh_34


title: FFD_veh_37


title: FFD_veh_33


title: FFD_veh_32


title: standard_diet_114

value: normal chow


title: FFD_veh_30


title: FFD_veh_31


title: standard_diet_113


title: standard_diet_111


title: FFD_veh_29


title: standard_diet_108


title: FFD_ACCi_1mpk_56-T


title: standard_diet_109


title: standard_diet_110


title: standard_diet_107


title: S222_MUSCLE_T715

status: Public on Apr 07 2020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Skeletal Muscle Sample from GESTALT Muscle Biopsies

data_processing:
Single-read sequencing was performed for 141 cycles and Real-Time Analysis (RTA) v1.18.66.3 generated the base-call files (BCL files). BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.17.1.14)
The quality of the bases was checked using FASTQC program (v11.2) before and after adapter removal and last base trimming by cutadapt program (v1.9).
The cleaned FASTQ files were aligned, quantified and annotated to the human hg19 genome using Salmon (Patro et al., 2017) with the concept of quasi-mapping with two phase inference procedure for gene model annotations.
Genome_build: human hg19 genome
Supplementary_files_format_and_content: .quant, TPM

source_name: Skeletal Muscle

extract_protocol:
Total RNA was prepared by lysing cell pellet (2x106) in 700ul Qiazol and extracted using Qiagen miRNeasy mini kit according to the manufacturer’s recommendation (Qiagen Inc, CA, USA)
Samples were prepared using Nugen Ovation v2 kits and the sequencing library was prepared using Illumina ChIP-Seq kits according to manufacturer’s protocol (Illumina, San Diego, CA).

value: Vastus lateralis

tag: age

tag: gender

value: Female


title: S223_MUSCLE_T595

value: Male


title: S221_MUSCLE_T610


title: S229_MUSCLE_T745


title: S224_MUSCLE_T625


title: S227_MUSCLE_T760


title: standard_diet_112

value: liver


title: S220_MUSCLE_T676


title: S231_MUSCLE_T790


title: S219_MUSCLE_T685


title: S217_MUSCLE_T520


title: S216_MUSCLE_T535


title: S215_MUSCLE_T505


title: S218_MUSCLE_T550


title: S214_MUSCLE_T490


title: S211_MUSCLE_T743


title: S213_MUSCLE_T475


title: S230_MUSCLE_T805


title: S226_MUSCLE_T730


title: S228_MUSCLE_T565


title: S212_MUSCLE_T445


title: S208_MUSCLE_T340


title: S225_MUSCLE_T580


title: S209_MUSCLE_T670


title: S207_MUSCLE_T640


title: S205_MUSCLE_T370


title: S203_MUSCLE_T430


title: S201_MUSCLE_T415


title: S121_MUSCLE_T290


title: S123_MUSCLE_T294


title: S119_MUSCLE_T298


title: S118_MUSCLE_T295


title: S120_MUSCLE_T296


title: S117_MUSCLE_T228


title: S115_MUSCLE_T300


title: S206_MUSCLE_T385


title: S202_MUSCLE_T355


title: S114_MUSCLE_T330


title: S204_MUSCLE_T400


title: S113_MUSCLE_T266


title: S111_MUSCLE_T329


title: S108_MUSCLE_T325


title: S106_MUSCLE_T232


title: S105_MUSCLE_T120


title: S101_MUSCLE_T293


title: S122_MUSCLE_T291


title: S102_MUSCLE_T326


title: S103_MUSCLE_T328


title: S107_MUSCLE_T297


title: e11.5_mouse_forelimb_WT_HOXA11_ChIPseq_rep1

status: Public on Mar 25 2020

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

data_processing:
ChIP-seq reads were aligned to the mm10 genome using bowtie v.2.3.1 with the following settings: bowtie2 -p 8 --fr --no-mixed --no-unal –x.
Sam files were converted into tag directories using HOMER v4.9.1 and into bam files using Samtools v1.4.1 view function.
bigwig files were generated using HOMER; Scores represent reads normalized per 10000000 reads
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: forelimb bud

extract_protocol:
HOXA11 ChIP was performed in forelimb buds of CD1 (wild type) and Prx1Cre; RosaHoxa11/Hoxa11 (RA11KI) mice at E11.5 in the same conditions as previously described for HOX13 ChIP 7. Chromatin was cross-linked using a combination of disuccinimidyl glutarate (DSG) and formaldehyde and sonicated using Fisher Scientific, Model 100 sonic dismembrator to obtain fragments between 100-600 bp. Protein A and Protein G Dynabeads (Invitrogen) were incubated for 6 hours at 4C with 5ug HOXA11 (SAB1304728, Sigma) antibody. The chromatin was coupled to the beads overnight at 4C. The immunoprecipitated samples were then sequentially washed in low salt (1% Triton, 0,1% SDS, 150 mM NaCl, 20 mM Tris (pH8), 2 mM EDTA), high salt (1% Triton, 0,1% SDS, 500 mM NaCl, 20 mM Tris pH8, 2 mM EDTA), LiCl (1% NP-40, 250 mM LiCl, 10 mM Tris (pH8), 1 mM EDTA) and TE buffer (50 mM NaCl, 10 mM Tris (pH8), 1 mM EDTA). The DNA was then purified on QIAquick columns (Qiagen).
Library and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendations and sequenced on Illumina Hiseq 2500 in a 50 cycles paired-end configuration.

value: mixed background C57Bl/6 x 129

value: WT

value: HOXA11 sigma:sab1304728

value: forelimb buds


title: control (dmso) sample 2

status: Public on Mar 28 2020

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

department: Biology

institute: Barnard College

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the A. mellifera reference genome available on NCBI using the STAR aligner.
The RNA-seq aligner is executed using a splice aligner, which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step.
Gene hit counts were calculated using Feature counts from the Subread package.
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2 and groups were compared.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: comma-separated values, normalized read ouns for paired samples

organism: Apis mellifera

source_name: honey bee midgut

extract_protocol:
Midguts were removed, stored in RNAlater, and RNA was harvested using Trizol reagent. RNA was submitted to additional quality control analysis before mRNA was enriched by polyA selectio
Llibrary preparation was performed using a NEBNext Ultra RNA library preparation kit. Sequencing was then performed using Illumina HiSeq platform.

treatment_protocol: Honey bees were fed sucose solution containning 24 uM Tunicamycin (0.5%DMSO) or 0.5% DMSO alone for 24 hours.

value: midgut

value: 0.5% DMSO alone for 24 hours


title: control (dmso) sample 3


title: S1117358_2: WT_APH_4

status: Public on Feb 28 2020

city: Tarrytown

first: Sandra

last: Kleiner

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals, Tarrytown, New York, USA

data_processing:
BCLs converted to Fastq performed using Cell Ranger v2.2
Reads were aligned to the GCRh37 genome assembly using Cell Ranger 3.0.2
Genome_build: GRCh37

source_name: differential ES cells

extract_protocol: SC-derived clusters at d27 were dissociated into single cells using TrypLE Express. The resulting dissociated cells were filtered through a 30 µm cell strainer and collected by centrifugation at 400 x g for 5 min. The cell pellet was resuspended in 5 mL 1X PBS containing 0.04% BSA and filtered through a 30 µm strainer. Cells were collected by centrifugation at 400 x g for 5 min and the pellet was resuspended with 1X PBS+0.04% BSA to a final concentration of 400-500 cells/µL. Total seq-A anti-human hashtag antibodies (BioLegend) were used for cell hashing. Each sample was individually stained with one of the hashtag antibodies and washed three times. Eight samples (4 Aph treated and 4 control samples) were pooled at equal concentrations, and the pool was loaded into the 10X Chromium instrument. Data from aphidicolin treated cells are marked Aph, and untreated cells are marked control according to the metadata sheet.

tag: cell type

value: ES-derived pancreatic beta cells

value: with/without APH (mixture)


title: S1117357_2: WT_APH_2


title: S1117358_1: WT_APH_3


title: S109_MUSCLE_T292


title: e11.5_mouse_forelimb_WT_HOXA11_ChIPseq_rep2


title: S104_MUSCLE_T230


title: 15163X2 Aged_wt

status: Public on Jan 31 2020

city: Salt Lake City

first: Ryan

middle: M.

last: O'Connell

state: UT

address: 15 N Medical Drive East, Emma Eccles Jones Medical Research Bldg, Rm 2100, Salt Lake City, UT 84112-5650

department: Pathology

institute: University of Utah

data_processing:
Demultiplex with cellranger mkfastq version 3.0.0 from 10x Genomics to create fastq files: I1 sample index, R1 cell barcode and UMI, R2 RNA sequence
Align reads to refdata-cellranger-mm10-3.0.0 from 10x Genomics and count barcodes and UMIs using cellranger count version 3.0.0 with expected-cells=5949
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MTX format from cellranger count.
Supplementary_files_format_and_content: cell_type_annotations.csv: Comma-separated text file including single-cell barcodes and computer-aided annotations of the cell types of the combined scRNAseq runs (4 total).

source_name: CD45+ splenocytes

extract_protocol:
Spleens were excised from euthanized animals and single cell suspensions were prepared using frosted ends of microscope slides and filtering through 40um nylon mesh. Samples were stained with anti-CD45-APC (Biolegend) antibody at 1:500 dilution in MACS buffer (PBS supplemented with 0.5% BSA and 2 mM EDTA). Live immune cells as defined by DAPI(-)CD45(+) staining pattern were FACS-sorted by using BD FACS Aria flow cytometer. Equal numbers of sorted cells were processed for single-cell 5' RNA-sequencing via 10X Genomics.
10X Genomics single cell 3-prime gene expression v2 chemistry library prep
Single-cell 3' RNA-Sequencing

tag: genotype/variation

value: aged

value: Spleen

value: CD45+ splenocytes


title: 15163X3 Aged_146ko


title: S1117357_1: WT_APH_1


title: 15163X1 Young_wt

value: young


title: S110_MUSCLE_T289


title: S112_MUSCLE_T331


title: cocaine-saline pooled_Iso-Seq

status: Public on Jan 16 2020

first: Li

last: Shen

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: cocaine and saline tissues were pooled without using multiplexing

data_processing:
Initial data processing was performed using the IsoSeq 3.1 software pipeline, which is incorporated into the online SMRTLink 8.0 bioinformatics tool suite (Pacific Biosciences). This pipeline error corrects sequencing reads through the generation of highly accurate (>99.9%, Q30) intramolecular circular consensus sequencing (CCS) reads. These CCS reads are then further processed to remove adapter sequences, trim polyA tails and remove concatemers for de novo identification of full length, high quality isoforms.
Due to the very low quantity of low quality reads, only high quality FASTQ data were used in this study. Gmap (version 2019-02-15) was run on the single high quality FASTQ file using the UCSC mm10 genome build, after which sorted SAM files were obtained. All uniquely-mapped isoforms were used as input into the TAMA Exon Cascade Collapse algorithm (version 2019-11-19) to reduce isoform redundancy.
Genome_build: mus musculus (mm10)
Supplementary_files_format_and_content: The GTF file represents the full-length, non-redundant, high-quality transcripts identified by Iso-seq; The CSV file represents the cluster report that accompanies the Iso-seq reads.

source_name: Nucleus Accumbens (NAc) from cocaine and saline treated mice

extract_protocol:
Nac were isolated one hour after the final injection and stored frozen at -80 until RNA extraction. RNA from individual mice was extracted using Qiagen RNeasy Mini kit and pooled prior to library preparation. NAc were isolated from each mouse bilaterally, so a total of 20 NAc punches were used for the experiment.
Long read isoform sequencing was performed according to the recommendations made in the Procedure and Checklist for Iso-Seq from Pacific Biosciences. We have applied Isoform Sequencing (IsoSeq) methods to the pooled sample. Briefly, two micrograms of high quality RNA (RIN = 8.8) was used as input into oligo-dT primed cDNA synthesis (Clontech). Following double-stranded cDNA amplification, transcripts were size selected, separating transcripts < 4 kb, from those > 4kb, using magnetic beads. The transcripts of each size bin were then equimolar pooled in order to adequately represent longer transcripts in the subsequent sequencing library. The pooled cDNA was then used as input into SMRTbell library preparation as recommended by the manufacturer. The SMRTbell library was sequenced on a SMRTcell 8M on the Sequel 2 platform using v2 chemistry, producing over 300 Gb of data.

treatment_protocol: Ten 8-10 week old male C57 mice were pooled to generate the RNA for sequencing. Five of the mice were given IP saline injections for 7 days, while the other 5 mice were given 20mg/kg cocaine via IP injection for 7 days. This was done to ensure that the reference transcriptome contained any splicing variants that might be induced only after cocaine exposure.

value: Nucleus Accumbens (NAc)

tag: Sex

value: 8-10 weeks


title: ON2

status: Public on Jan 13 2020

city: Ann Arbor

first: Marina

last: Pasca Di Magliano

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

description:
Whole iKras orthotopic tumor digested to single cell suspension and submitted for single cell sequencing
Mouse_On_Merge_Fil.Rdata, ON2_raw_gene_bc_matrices_h5.h5

data_processing:
BCL files were generated by Illumina sequencers
BCL files were demultiplexed into FASTQ files using cellranger mkfastq (v2.1.1 for Samples 1 and 2 and v3.0.0 for Sample 4)
FASTQ files were aligned, filtered and counted by cellranger count (v2.1.1 for Samples 1 and 2 and v3.0.0 for Sample 4) and formed into feature-barcode matricies
Feature-barcode matricies were read into R using Seurat and were analyzed according to the Seurat pipeline, including normalizing, scaling,  filtering based on counts and mitochondrial gene percentage, and labeling according to gene expression profiles
Genome_build: mm10

source_name: iKras orthotopic tumor

extract_protocol:
Single cells were digested from tissues by mechanical digestion of tissue followed by incubation in a digestion buffer made of 1 mg/mL collagenase, 20 μg/mL hyaluronidase, 50 μg/mL DNase Type I, in RPMI + 1% FBS. The cells were then passed through a 40 μm cell strainer. Dead cells were removed using MACS® Dead Cell Removal Kit.
The single cells were run on the 10X Genomics Chromium platform, resulting in a barcoded cDNA library.

value: FVBN

tag: ikras status

value: Kras induced

tag: time point

value: 2 weeks 3 days ON

tag: number of mice pooled

tag: treatment protocol

value: Mice were fed doxycycline chow to induce expression of KrasG12D

tag: solo/merged file

value: Solo


title: ON1

description:
Whole iKras orthotopic tumor digested to single cell suspension and submitted for single cell sequencing
Mouse_On_Merge_Fil.Rdata, ON1_raw_gene_bc_matrices_h5.h5

tag: strain


title: ML292  CON

status: Public on Nov 23 2019

city: Boston

first: Annie

last: Kathuria

state: MA

address: 185 cambridge street

institute: Mass Gen Hospital

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: 2D cortical neurons

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R

value: Human iPSC derieved cerebral organoids

value: 3 months of differentiation

tag: diagnosis

value: healthy control


title: ML300  CON


title: ML135  CON


title: WT rep2 [WTCHG_337412_289112]

extract_protocol:
Total RNAs were extracted by a standard hot phenol method.
NEBNext ultra II directional RNA library prep kit for Illumina

tag: strain background

value: Wild-type


title: ML51  CON


title: ML126  CON


title: ML27 CON


title: 15163X4 Aged_146ko_155tcko

tag: tissue


title: JR1832: KO-8

status: Public on Oct 03 2019

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Avenue

institute: University of Colorado Boulder

data_processing:
Read 1 was trimmed by piping cutadapt: "cutadapt -u 3 - | cutadapt -a AAAAAAAA - | cutadapt -a AAAAAAAN$ -a AAAAAAN$ -a AAAAAN$ - | cutadapt -a AGAGCACACGTCTG - "
Read 2 was trimmed by piping cutadapt: "cutadapt -g TTTTTTTT - | cutadapt -g ^NTTTTTTT -g ^NTTTTTT -g ^NTTTTT - | cutadapt -a CCCGATCGTCGG - | cutadapt -a GGGGATCGTCGG -"
The adapter-trimmed reads were mapped to the mm10 mouse reference genome using TopHat v2.1.1 with the flags: "--no-coverage-search --GTF gencode.vM9.annotation.gtf"
Uniquely-mapped reads were counted for genes by featureCounts
Transcripts per million was calculated
Genome_build: mm10
Supplementary_files_format_and_content: Comma seperated file

source_name: Commom Lymphoid Projenitor

extract_protocol:
RNA was isolated using RNeasy micro columns (Qiagen) on a QIAcube (Qiagen) after TRIzol treatment.
Poly(A)+ RNA-seq libraries were constructed using CATS RNA-seq kit v2 (Diagenode, C05010041).

value: Commom Lymphoid Projenitor

value: Male

tag: genotype

value: KO


title: JR1839: WT-6

value: WT


title: JR1700: R-4

value: Rescue


title: JR1842: KO-9


title: JR1694: R-2


title: JR1840: WT-10


title: JR1843: KO-12


title: JR1697: R-3


title: HEK TE VP10_4

status: Public on Aug 13 2019

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Library strategy: 4C-seq
We used PeakC for calling of near-cis interaction and our custom scripts for calling of far-cis (>5 MB from the viewpoint; https://github.com/ZhaoPeiHua/LongRangeInteraction_from_4C-seq) and trans interaction. PeakC was incorporated in the pipeline  pipe4C . The pipeline performed reads demultiplexing, trimming, mapping, and counting in one step directly from FASTQ files. The default settings were used. The pipeline stored the reads mapping statistics as RDS file, which was further processed by the function  doPeakC  from the pipeline for the near-cis peak calling. The far-cis (>5 MB from the viewpoint) and trans interactions were analyzed using our custom scripts. The reads were demultiplexed by the reading primer in the 5  end. Each PCR primer represented a single 4C experiment. The reading primer was then trimmed from the reads. Primer trimmed-reads were mapped to hg38 assembly by STAR, and the multi-mapping reads were excluded from the bam files. A library of restriction fragment ends was constructed based on DpnII restriction sites. The mapped reads that do not start at DpnII restriction sites were discarded. The reads were counted per fragment end, and only fragment ends with at least two mapped reads were considered as an observed one. To correct for PCR artifacts, fragment ends coverages were binarized (observed and non-observed fragment end is set to 1 and 0, respectively). To identify significant interactions, a sliding window of 400 fragment ends was used to count observed fragment ends and the whole chromosome was used as background window to count the observed fragment end, a binomial test was applied to test the null-hypothesis that the proportion of observed fragment ends in a window was below or equal to the background proportion. The regions near (<5 MB) the viewpoint were masked out. P-values were adjusted using the Benjamini-Hochberg procedure. Windows with an adjusted p-value<0.05 were scored as significant interactions.
Genome_build: HG38

source_name: human embryonic kidney cells

growth_protocol: HEK TE cells were cultured in DMEM (Thermofisher), supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Cells nuclei were cross-linked with formaldehyde and treated with a primary 4-bp restriction endonuclease, DpnII. Ligation of digested DNA was performed followed by removal of chromatin crosslinks. A final round of digestion was performed using a secondary 4-bp restriction endonuclease, CviQI, trimming the DNA. Finally, ligation of the DNA fragments circular DNA was performed. Captured DNA containing target loci was amplified by inverse PCR, using primers designed for the flanking sequences of each viewpoint, and sent for next-generation sequencing generating approximately 1 million 50bp single end reads.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown to 70-80% confluency before harvesting.

tag: cell line

value: HEK TE

value: human embryonic kidney cells


title: JR1691: R-1


title: HEK TE VP10_3


title: HEK TE VP10_2


title: ML56  CON


title: HEK TE VP10_1


title: HEK TE VP9


title: HEK TE VP8


title: JR1833: KO-11


title: HEK TE VP7


title: HEK TE VP6


title: JR1831: WT-11