title: Profiling of RNA from rRNA-depleted RNA library from treated liver metastases [T-LM_5]

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

institute: University of Regensburg

data_processing:
Base calling was performed using CASAVA 1.8.2 software
Differential gene expression analysis:
Raw reads were mapped to the human genome (hg38 assembly) using STAR version 2.7.0a with --outFilterMultimapNmax 2000000000 and --outSAMmultNmax 1 settings. Reads were counted using Rsubread 1.34.7 with Ensembl release 98 genome annotation reference.
Differential expression analysis was performed within R using DESeq2 version 1.24.0.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files including count tables and DESeq2 outputs

source_name: Treated Liver metastases (T-LM)

growth_protocol: HT29 cells were cultivated in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 µg/mL streptomycin. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
Tumor samples (PT and LM) were cutted into smaller pieces before putting them into the lysing matrix tubes, type "D" (MP Biomedicals). Tubes with 1 ml TRIzol (Invitrogen) were cooled on ice before samples were added. Tumors were homogenized using Fastprep-24-System with 1x 45 sec. @ full speed in TRIzol. After homogenisation, total RNA from tumor samples was isolated according to TRIzol's protocol. Total RNA from HT29 cells was isolated using TRIzol according to TRIzol's protocol without homogenisation steps.
Workflow consists of double-stranded cDNA generation using a customizable mixture of random and poly(T) priming, fragmentation of double-stranded cDNA, end repair to generate blunt ends, adaptor ligation, strand selection via nucleotide analog-targeted degradation, InDA-C-mediated adaptor cleavage and PCR amplification to produce the final library. The detailed protocol can be found at the user guide Ovation Human FFPE RNA-Seq System.

treatment_protocol: Three SCID mice were initially used for tumor development to collect RNA for RNA sequencing (RNA-seq) via intrasplenic implantation. HT29 cells were dissociated with trypsin, washed once with DMEM supplemented with 10% FCS, 1% PS and then resuspended to the desired concentration in Hank's Balanced Salt Solution (HBSS, Sigma). All animals receiving tumor cell injections were injected with the same quantity of cells (500 000 cells per animal). Abdominal access was obtained via a left subcostal skin and peritoneal wall incision. The spleen was gently exteriorized. 5 µl of 500 000 tumor cells were injected with a 10 µl Hamilton syringe (BD Biosciences). The needle was slowly retracted and the injection site pressed with a moist cotton swab to prevent leakage. The spleen was returned to the peritoneal cavity; peritoneum and skin were closed by running sutures and wound clips. Bioluminescence measurement was performed weekly or every 3 days. For this purpose, mice were anaesthetized, injected with 100 µl of 30 mg/ml D-luciferin (Biosynth, Staad, Switzerland) for 3 min, and emitted photons were registered for 3 min using Xenogen IVIS Lumina Imaging System (Caliper Life Sciences). Primary tumor (either subcutaneous tumor or in spleen) and metastases in the liver resections were performed when the tumor size was big enough or when the bioluminescence measurement was significant. All tumors were collected in RNAlater (Thermo Scientific).

value: Liver metastases from LDM topotecan treated mice


title: H3K4me3_LC_NCI-H23

status: Public on Jan 21 2021

type: SRA

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

country: USA

institute: Wayne State University

description: Chromatin IP against H3K4me3

library_source: genomic

data_processing:
Sequence reads were obtained and mapped to the human (hg19) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: NCI60 cancer cells were cultured in RPMI 1640 / 5% FBS media containing glutamine and pen/strep at 37oC with 5% CO2. Cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: cell line

tag: cell type

value: cancer cell

tag: antibody

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: H3K4me3_LE_K-562

description: Chromatin IP against H3K4me3


title: 59d-plus-21DIV

city: Happy Valley

first: Alex

middle: Daniel

last: Chitsazan

state: OR

address: 2720 S Moody Ave

institute: Oregon Health and Science University

library_source: transcriptomic

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were mapped to GRCh38 whole genome using HISATv2.1.0 with parameters --max-intronlen 500000 -p 11
Gene counts were called using HTSeq-count using the mode intersection-strict
Genome_build: GRCh38
Supplementary_files_format_and_content: hts files contain counts tables for each sample

molecule: total RNA

source_name: Retina

growth_protocol: Stem cell were differentiated with modifications to Meyer et al. 2009 protocol.  Fetal retinal explants were grown on filters using the retinal medium (Methods)

extract_protocol:
All samples were extracted in TRIzol. RNA from these was purified using Qiagen Rneasy Micro kit and was used for RNAseq analysis. Genomic DNA of the retinas was precipitated from the interphase and phenol phase of the TRIzol solution using 100% ethanol. The DNA pellet was washed 3 times with 0.1 M sodium citrate/10% ethanol solution and once with 75% ethanol. The pellet was then resuspended in 8 mM NaOH buffer or concentrated using gDNA Clean and Concentrator kit (Zymo Research, Irvine, CA). . Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Following the desulphonation and wash steps, converted DNA was eluted in 12 µl of the M-Elution buffer  and was used for epigentic clock analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age at dissection (day)

tag: days in vitro

tag: tissue origin

value: fetal

tag: karyotype

value: WT

tag: tissue

value: retina


title: HEK293T_GFP-hTLX

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

data_processing:
Quality control of raw RNA-seq reads was performed prior to assembly using FastQC (0.11.5), followed by trimming and filtering of the reads with TrimGalore (0.3.3) to remove adapter sequences and reads with Phred quality scores below 20.
Counts and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using HtSeq (0.6.1)(60) and Cufflinks (2.2.1)(61).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HEK 293T cells

extract_protocol:
Total RNA was extracted with Total RNA Purification Plus Kit (Norgen Biotek Corp.) with DNase I treatment, according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer and RNA quantification with Nanodrop and Qubit.
Illumina TruSeq strand-specific RNA libraries (Ribosomal depletion using RiboZero human) containing 125 bp pair-end reads were obtained for each sample on a HiSeq2000 sequencer (Illumina) using standard Illumina protocols.

tag: vector

value: eGFP-hTLX

tag: vector induced

value: Yes


title: H3K4me3_LC_HOP-62

description: Chromatin IP against H3K4me3


title: D113T21

value: Trisomy 21


title: 59d-plus-ODIV


title: H3K4me3_LC_NCI-H522

description: Chromatin IP against H3K4me3


title: H3K4me3_LE_CCRF-CEM

description: Chromatin IP against H3K4me3

source_name: CCRF-CEM

value: CCRF-CEM


title: H3K4me3_LC_EKVX

description: Chromatin IP against H3K4me3

source_name: EKVX

value: EKVX


title: H3K4me3_LC_NCI-H460

description: Chromatin IP against H3K4me3


title: HEK293T_GFP

value: eGFP


title: Mock.plus.CPA

city: Duarte

first: John

middle: P.

last: Murad

state: California

address: 1500 E. Duarte Rd

institute: City of Hope

description:
stranded KAPA mRNA HyperPrep library
RNA-Seq data, Mock, CPA Treatment

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq (version 2.18) was used for base calling.
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search (with --library-type fr-firststrand for stranded library samples)
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Mmusculus.UCSC.mm10.knownGene (Bioconductor annotations, downloaded 8/30/2018).  Strand for htseq-count was to  "reverse" to match the library type.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM normalized expression (using genome-aligned reads and TxDb annotations in R) and read counts (calculated using htseq-count)

organism: Mus musculus

source_name: RNA collected from subcutaneous RM9 tumor lysate

growth_protocol: Prior to engraftment cells grown in complete DMEM media. RNA was collected directly from harvested subcutaneous tumors from each treatment group.

extract_protocol:
Lysate was then chloroform extracted for RNA and purified via a Qiagen RNA Easy isolation kit (Qiagen) according to manufacturer’s protocol
KAPA stranded polyA kit
stranded polyA RNA-Seq

treatment_protocol: Tumor bearing mice were treated 6 days after tumor engraftment with or without cyclophosphamide (100mg/kg ; i.p.) then treated with Mock or CAR T cells on day 7, tumors harvested 3 days later (day 10 post engraftment).

tag: treatment

value: Mock, CPA Treatment

value: subcutaneous RM9 tumor lysate


title: CAR

description:
stranded KAPA mRNA HyperPrep library
RNA-Seq data, CAR-T, No CPA Treatment

value: CAR-T, No CPA Treatment


title: H3K4me3_LC_A549

description: Chromatin IP against H3K4me3


title: CAR.plus.CPA

description:
stranded KAPA mRNA HyperPrep library
RNA-Seq data, CAR-T, CPA Treatment

value: CAR-T, CPA Treatment


title: Profiling of RNA from rRNA-depleted RNA library from treated liver metastases [T-LM_4]

country: Germany


title: H3K4me3_LC_HOP-92

description: Chromatin IP against H3K4me3


title: iPSC_M14939#3_medips_rep1

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Baboon MeDIP-seq reads files were mapping to UCSC papAnu4 by Rsubread with default parameters.
After mapping to the reference genome, bam files of repicates were merged by samtools-1.10. Duplicated reads were marked by Picard-2.239, then removed from the downstream analysis by samtools. Uniquely mapped reads were sorted by samtools-1.10.
MACS2 was used for  reads filteration, fragments length prediction and peak calling.
Deeptools bamcoverage was used for  making bigwig files and heatmap analysis.
Genome_build: papAnu4
Supplementary_files_format_and_content: peak filles generated by MACS2
Supplementary_files_format_and_content: bigwig files, generated by Deeptools

organism: Papio anubis

source_name: iPS line M14939#3

growth_protocol: Baboon (Papio anubis) ES (B4, B15) and iPS (160-2, M14939#3) cells used in this study were previously derived (Navara et al., 2013) and grown on feeder cells at 37°C/5% CO2 in PluriSTEM™ Human ES/iPS Medium as described (Navara et al., 2018).

extract_protocol: MeDIP-seq libraries were prepared by following the previously published protocol. Taiwo, O., Wilson, G., Morris, T. et al. Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc 7, 617–636 (2012). https://doi.org/10.1038/nprot.2012.012

value: Induced pluripotent stem cells

value: 5-methylcytosine (5-mC) Antibody, (diagenode, Mab-081-110)

value: iPS line M14939#3


title: iPSC_M14939#3_medips_rep2

source_name: iPS line M14939#5

value: iPS line M14939#5


title: iPSC_M14939#3_medips_Input_rep1

source_name: iPS line M14939#4

value: input

value: iPS line M14939#4


title: 18A0983

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

description: RNA extracted from FFPE tissue

data_processing:
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Genome_build: mm9
Supplementary_files_format_and_content: comma-separated value file includes filtered raw read counts for each gene_probe

source_name: FFPE liver

growth_protocol: Female B6D2F1/Crl mice were bred at Charles River Laboratories.

extract_protocol:
Formalin-fixed, paraffin-embedded liver tissue was scraped from sections mounted to glass slides directly into lysis buffer.
The TempO-Seq (BioSpyder Technologies) RNA sequencing protocol was followed for library construction: mRNA targets were hybridized with a detector oligomer probe mix, excess oligos are removed, followed by detector oligo ligation.

treatment_protocol: B6D2F1/Crl mice exposed to 0, 40, 200, 600, 2000, or 6000 pmm 1,4-dioxane continuously in drinking water for 7, 28, or 90 days.

tag: strain

value: liver

tag: time

tag: genotype

value: wildtype


title: iPSC_M14939#3_medips_Input_rep3

source_name: iPS line M14939#8

value: iPS line M14939#8


title: iPSC_M14939#3_medips_rep3

source_name: iPS line M14939#7

value: iPS line M14939#7


title: iPSC_160-2_medips_Input_rep2

source_name: iPS line 160-2

value: iPS line 160-2


title: iPSC_M14939#3_medips_Input_rep2

source_name: iPS line M14939#6

value: iPS line M14939#6


title: H3K4me3_CO_KM12

description: Chromatin IP against H3K4me3

value: cancer cell

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: Mock

description:
stranded KAPA mRNA HyperPrep library
RNA-Seq data, Mock, No CPA Treatment

value: Mock, No CPA Treatment

value: subcutaneous RM9 tumor lysate


title: H3K4me3_LC_NCI-H322M

description: Chromatin IP against H3K4me3


title: H3K4me3_LC_NCI-H226

description: Chromatin IP against H3K4me3


title: 18A0981

description: RNA extracted from FFPE tissue


title: iPSC_160-2_medips_Input_rep1


title: H3K4me3_CO_SW-620

description: Chromatin IP against H3K4me3


title: iPSC_160-2_medips_rep3


title: 18A0982

description: RNA extracted from FFPE tissue


title: ESC_B15_medips_Input_rep2

source_name: ES line B15

value: Embryonic Stem Cells

value: ES line B15


title: iPSC_160-2_medips_rep2

value: Induced pluripotent stem cells

value: 5-methylcytosine (5-mC) Antibody, (diagenode, Mab-081-110)


title: ESC_B15_medips_rep2


title: H3K4me3_CO_HCT-116

description: Chromatin IP against H3K4me3


title: 18A0979

description: RNA extracted from FFPE tissue


title: 18A0953

description: RNA extracted from FFPE tissue


title: iPSC_160-2_medips_rep1


title: H3K4me3_CO_HT29

description: Chromatin IP against H3K4me3


title: 18A0980

description: RNA extracted from FFPE tissue


title: ESC_B15_medips_Input_rep3


title: H3K4me3_CO_HCT-15

description: Chromatin IP against H3K4me3


title: ESC_B15_medips_rep3


title: ESC_B15_medips_rep1


title: 18A0952

description: RNA extracted from FFPE tissue


title: H3K4me3_CO_HCC-2998

description: Chromatin IP against H3K4me3


title: iPSC_160-2_medips_Input_rep3


title: ESC_B15_medips_Input_rep1


title: H3K4me3_CO_COLO_205

description: Chromatin IP against H3K4me3

source_name: COLO 205

value: COLO 205


title: 18A0951

description: RNA extracted from FFPE tissue


title: ESC_B4_medips_Input_rep3

source_name: ES line B4

value: input

value: ES line B4


title: ESC_B4_medips_Input_rep2


title: ESC_B4_medips_rep3


title: ESC_B4_medips_rep2


title: ESC_B4_medips_rep1


title: 18A0950

description: RNA extracted from FFPE tissue

value: liver


title: H3K4me3_CNS_SNB-75

description: Chromatin IP against H3K4me3


title: H3K4me3_CNS_U251

description: Chromatin IP against H3K4me3


title: iPSC_M14939#3_ChIP_Input_rep3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Baboon ChIP-seq reads files were mapping to UCSC papAnu4 by Rsubread with default parameters.
After mapping to the reference genome, bam files of repicates were merged by samtools-1.10. Duplicated reads were marked by Picard-2.239, then removed from the downstream analysis by samtools. Uniquely mapped reads were sorted by samtools-1.10.
MACS2 was used for  reads filteration, fragments length prediction and peak calling.
Deeptools bamcoverage was used for  making bigwig files and heatmap analysis.
Genome_build: papAnu4
Supplementary_files_format_and_content: peak filles generated by MACS2
Supplementary_files_format_and_content: bigwig files, generated by Deeptools

extract_protocol: ChIP-Seq libraries were prepared with antibodies for H3K4me3 (abcam8580), H3K9me3 (abcam8898), H3K27me3 (abcam6002), and H3K27ac (39133, Active Motif, Carlsbad, CA). Each library was prepared from 50,000 cells with inclusion of PEG in samples during MNase digestion, adapter ligation with NEB adapters (E7535S, New England Biolabs, Ipswich, MA) and adapter cleavage by incubation with USER enzyme (M5505S, New England Biolabs) at 37°C for 15 min.

value: iPS line M14939#3


title: ESC_B4_medips_Input_rep1


title: iPSC_M14939#3_ChIP_Input_rep1


title: iPSC_160-2_ChIP_Input_rep3


title: iPSC_M14939#3_ChIP_Input_rep2


title: H3K4me3_CNS_SNB-19

description: Chromatin IP against H3K4me3


title: H3K4me3_CNS_SF-539

description: Chromatin IP against H3K4me3


title: iPSC_160-2_ChIP_Input_rep2


title: H3K4me3_CNS_SF-295

description: Chromatin IP against H3K4me3


title: ESC_B15_ChIP_Input_rep3


title: iPSC_160-2_ChIP_Input_rep1


title: 18A0921

description: RNA extracted from FFPE tissue

value: wildtype


title: ESC_B15_ChIP_Input_rep1


title: 18A0920

description: RNA extracted from FFPE tissue


title: H3K4me3_CNS_SF-268

description: Chromatin IP against H3K4me3


title: H3K4me3_BR_T-47D

description: Chromatin IP against H3K4me3


title: ESC_B15_ChIP_Input_rep2


title: ESC_B4_ChIP_Input_rep3


title: ESC_B4_ChIP_Input_rep1


title: 18A0893

description: RNA extracted from FFPE tissue


title: 18A0923

description: RNA extracted from FFPE tissue


title: ESC_B4_ChIP_Input_rep2


title: 18A0919

description: RNA extracted from FFPE tissue


title: 18A0922

description: RNA extracted from FFPE tissue


title: 18A0949

description: RNA extracted from FFPE tissue


title: iPSC_M14939#3_H3K9me3_rep2


title: H3K4me3_BR_MDA-MB-231

description: Chromatin IP against H3K4me3


title: 18A0891

description: RNA extracted from FFPE tissue


title: iPSC_M14939#3_H3K9me3_rep1


title: H3K4me3_BR_MCF7

description: Chromatin IP against H3K4me3


title: H3K4me3_BR_MDA-MB-468

description: Chromatin IP against H3K4me3


title: 18A0890

description: RNA extracted from FFPE tissue


title: iPSC_160-2_H3K9me3_rep2


title: iPSC_160-2_H3K9me3_rep3


title: H3K4me3_BR_HS_578T

description: Chromatin IP against H3K4me3

source_name: HS 578T

value: HS 578T


title: 18A0889

description: RNA extracted from FFPE tissue


title: iPSC_M14939#3_H3K4me3_rep2


title: iPSC_160-2_H3K9me3_rep1

value: iPS line 160-2


title: iPSC_M14939#3_H3K4me3_rep3


title: H3K4me3_BR_BT-549

description: Chromatin IP against H3K4me3


title: 18A0863

description: RNA extracted from FFPE tissue


title: iPSC_160-2_H3K4me3_rep3


title: 18A0862

description: RNA extracted from FFPE tissue


title: iPSC_M14939#3_H3K4me3_rep1


title: iPSC_160-2_H3K4me3_rep2


title: iPSC_M14939#3_H3K9me3_rep3


title: iPSC_M14939#3_H3K27me3_rep2


title: 18A0861

description: RNA extracted from FFPE tissue


title: iPSC_160-2_H3K4me3_rep1


title: iPSC_M14939#3_H3K27me3_rep3


title: 18A0860

description: RNA extracted from FFPE tissue


title: R3_B_TN_7

city: Bethesda

first: Nataliya

middle: Prokopenko

last: Buxbaum

state: Maryland

address: 10 Center Drive, CRC, 3-3288

department: ETIB

institute: NCI, NIH

data_processing:
Reads were trimmed of low-quality bases and adapter sequences were removed using Trimmomatic v0.33
Mapping of reads to the GRCh37 (hg19) mouse reference genome was performed using STAR v2.5.2b in 2-pass mode
RSEM v1.3.0 was used to quantify gene-level expression, with counts normalized to library size as counts- per-million
limma-voom v3.34.5 was used for quantile normalization and differential expression
Genome_build: Gencode mm10 M12 release
Supplementary_files_format_and_content: 2 Excel files including CPM TPM, FKPM and TPM counts for each sample, and a combined file with differential expression of CD4 Tn vs. Tem (3 samples combined)

source_name: FACS-purified CD4 T cells

extract_protocol:
Single-cell suspensions of spleen cells were obtained by mechanically disrupting harvested spleens and filtering through 70-μm mesh filters (Thermo Fisher Scientific). Ammonium-chloride potassium (ACK) lysis was performed to remove erythrocytes prior to cell counting. One million to two million live cells were aliquoted for flow cytometry staining. For fluorescence-activated cell sorting (FACS), samples from multiple mice were pooled for each cohort (allogeneic CD4+ Tn and Tem cells). Tn cells were defined as CD4+CD1d-CCR7+CD44low and Tem cells as CD4+CD1d-CCR7-CD444high. Pooled samples for each cohort underwent FACS using BD Influx achieving 95% purity. FACS-purified samples were collected into PBS buffer containing 2% (v/v) BSA. RNA was extracted from sorted cell populations using the RNeasy® Plus Mini Kit following the manufacturers protocol for purification of total RNA from animal cells (Qiagen). In brief, the cells were lysed in Buffer RLT Plus with Beta-ME, homogenized with a QIAshredder spin column, and the resultant lysate was run through a gDNA Eliminator spin column to remove genomic DNA. RNA was extracted by passing the remaining lysate through a RNeasy spin column and, following washes, total RNA was resuspended in 30 µl of RNase-free water. Measurement of RNA concentration and quality control was performed using a 2100 Bioanalyzer instrument with the standard manufacturers protocol (Agilent).
RNA-Seq libraries were constructed from 0.1-0.6 µg total RNA. The HyperPrep RNA-Seq Kit with Riboerase (Kapa Biosystems/Roche) was used according to manufacturer’s instructions to deplete rRNA and then construct libraries for sequencing on Illumina platforms. Amplification was performed using 10 or 12 cycles which was optimized for the input amounts and to minimize the chance of over-amplification. Unique barcode adapters were applied to each library. Libraries were pooled in equimolar ratio for sequencing. The pooled libraries were sequenced on multiple lanes of a HiSeq 4000 using achieve a minimum of 65 million 75 base read pairs. The data was processed using RTA version 1.18.54 and CASAVA 1.8.2.

treatment_protocol: Recipient female mice at 12-13 weeks of age were conditioned with 850 cGy total body irradiation (TBI) delivered in two doses 3 hours apart on day -1. Age-matched female B10.D2 mice were used for as donors for allogeneic transplants. Recipients were reconstituted with 15 million unfractionated splenocytes and 8 million bone marrow cells injected via tail vein on day 0. The injection buffer contained gentamicin (100 μg/ml), however no additional antibiotics were administered post-transplant. Animals were weighed and cGvHD scoring was performed twice weekly using a previously described clinical scoring system (Anderson, 2003)

tag: day post transplant

tag: graft donor strain

tag: graft recipient strain

value: BALB/c

value: spleen

value: CD4 Tn


title: R2_B_TEM_3

value: CD4 Tem


title: iPSC_M14939#3_H3K27me3_rep1

tag: cell line


title: iPSC_160-2_H3K27me3_rep2

tag: cell type


title: iPSC_160-2_H3K27me3_rep3

tag: antibody


title: R1_B_TEM_1


title: 18A0833

description: RNA extracted from FFPE tissue


title: iPSC_160-2_H3K27me3_rep1


title: 18A0859

description: RNA extracted from FFPE tissue


title: iPSC_M14939#3_H3K27ac_rep2


title: iPSC_M14939#3_H3K27ac_rep3


title: iPSC_M14939#3_H3K27ac_rep1


title: 18A0832

description: RNA extracted from FFPE tissue


title: L3mbtl2KO2

city: Nanjing

first: Su

last: Ting

address: No. 12, Xuefu Road, Pukou District

department: Model Animal Research Center

institute: Nanjing University

data_processing:
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non-biological replicates.
Genome_build: GRCm38.91
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values for each Sample.

source_name: Embryonic stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA purity was checked using the Qubit® 3.0 Fluorometer (Life Technologies, CA, USA); RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA); A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Embryonic stem cells


title: iPSC_160-2_H3K27ac_rep3


title: R3_B_TEM_5


title: 18A0831

description: RNA extracted from FFPE tissue


title: L3mbtl2KO1


title: 18A0830

description: RNA extracted from FFPE tissue


title: MgaKO3

value: Mga-/-


title: iPSC_160-2_H3K27ac_rep2


title: MgaKO2


title: 18A0829

description: RNA extracted from FFPE tissue


title: ESC_B15_H3K9me3_rep3

value: Embryonic Stem Cells

value: ES line B15


title: Pcgf6KO2


title: Pcgf6KO1


title: 18A1003

description: RNA extracted from FFPE tissue


title: MgaKO1


title: WT2

value: wild type


title: 18A1001

description: RNA extracted from FFPE tissue


title: 18A1002

description: RNA extracted from FFPE tissue


title: ESC_B4_H3K9me3_rep3


title: 18A1000

description: RNA extracted from FFPE tissue


title: WT1


title: 18A0999

description: RNA extracted from FFPE tissue


title: ESC_B4_H3K9me3_rep2


title: ESC_B4_H3K9me3_rep1


title: iPSC_160-2_H3K27ac_rep1

value: Induced pluripotent stem cells


title: ESC_B15_H3K9me3_rep2


title: WT3


title: Non-beating SVF rep2

type: RNA

city: Kanazawa

first: Shinichiro

last: Takashima

address: 13-1 Takara-machi

department: Cardiovascular Medicine

country: Japan

institute: Kanazawa University

description: Gene expression data from the non-beating SVF

hyb_protocol: 5 ug of cDNA were hybridized for 18 hr at 45C on the GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000-7G.

data_processing: The data were analyzed with BRB Array Tools software (v. 4.6.0)

label: biotin

source_name: Non-beating SVF

label_protocol: Biotinylated cDNA were prepared according to the Nugen protocol  (Tecan Genomics, Inc., Maennedorf, Switzerland).

growth_protocol: Isolated adipose tissue-derived SVF cells were seeded on a standard uncoated tissue culture plate (Nunc) (Thermo Fisher Scientific) in the minimal medium consisting of IMDM (I3390, Sigma-Aldrich), 10% FBS, 2 mmol/L L-glutamine (Wako, Osaka, Japan), 100 units/mL penicillin, 100 µg/mL streptomycin, and 0.1 mmol/L 2-mercaptoethanol (StemSure) (Wako) at a density of 5000 live cells/cm2 and cultured under standard conditions (37°C with 5% CO2). The culture medium was changed twice weekly for 4 weeks.

extract_protocol: Total RNA was processed to generate sense-strand cDNA (ss-cDNA) using the Ovation Pico RNA WTA System (Tecan Genomics, Inc., Maennedorf, Switzerland).

treatment_protocol: The cells were not treated in particular during the course of primary culture of SVF except the minimal growth medium. All of the beating SVF colonies in a dish on day 28 were manually picked up and combined, constituting the beating SVF (beating) group. Other cells were collected as the non-beating SVF (non-beating) group. To test our hypothesis that the round cells were the progenitors of CMs, we performed a single-cell-based global gene expression analysis. At day 14 of primary SVF culture, six round cells were picked up using the ALS CellCelector system and combined for microarray analysis.

tag: age

value: 10 weeks

tag: tissue source

value: subcutanous adipose tissue

value: Non-beating SVF


title: Non-beating SVF rep3


title: 18A0993

description: RNA extracted from FFPE tissue

value: liver


title: Sample_110: DLBCL tissue RNA

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark. CpG-context methylation call output files are in txt format and filtered for at least 10 covered cytosines per site. Tab-delimited csv file includes Kallisto TPM values for protein-coding genes for RNA-sequenced samples
Illumina Casava-1.8.2 software used for basecalling

source_name: DLBCL tumor sample

extract_protocol: trizol extraction and TruSeq RNA sample prep kit.

value: Diffuse large B-cell lymphoma (DLBCL)


title: Sample_110: DLBCL tissue eRRBS

extract_protocol: enhanced reduced representation bisulfite sequencing method (eRRBs) was followed as reported in Garrett-Bakelman et al 2015 doi: 10.3791/52246


title: Non-beating SVF rep4


title: ESC_B15_H3K4me3_rep3


title: ESC_B15_H3K4me3_rep2


title: Round SVF cell

description: Gene expression data from the round SVF cell

source_name: Round SVF cell

value: Round SVF cell


title: Non-beating SVF rep1


title: Sample_109: DLBCL tissue eRRBS


title: IL-1beta Runx2-input

city: Bunkyo-ku

first: Kosei

last: Nagata

state: Tokyo

department: Graduate School of Medicine

institute: the University of Tokyo

data_processing:
GENEWIZ
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v2.2.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Our peak predictions are performed using a modified version of the cisGenome peak caller named “SingleChIPSeq_fromPOS_linux_64_bit”.
The most stringent way to detect peaks is to perform a 2‐sample analysis where background signal is determined via an input control or mock IP.
Genome_build: mm9
Supplementary_files_format_and_content: nearet genes text files

source_name: Primary chondrocytes

growth_protocol: Primary chondrocytes were isolated as previously described (Gosset M, 2008. Nat Protoc).

extract_protocol:
ChIP were performed following the previous report (Ohba S, Cell Report. 2015).
DNA libraries were prepared for sequencing Illumina reccomended protocols

treatment_protocol: Culture with or without IL-1beta 1ng/microL.

value: culture with IL-1beta


title: IL-1beta Runx2-IgG

value: Anti-Mouse-IgG (PROMEGA; W4028)


title: IL-1beta Runx2-FLAG

value: Anti-FLAG M2 (SIGMA; F3165)


title: Sample_109: DLBCL tissue RNA


title: 18A0990

description: RNA extracted from FFPE tissue

value: wildtype


title: 18A0992

description: RNA extracted from FFPE tissue


title: ESC_B4_H3K4me3_rep3

value: ES line B4


title: 18A0989

description: RNA extracted from FFPE tissue


title: Sample_108: DLBCL tissue RNA


title: Beating SVF rep4

description: Gene expression data from the beating SVF

source_name: Beating SVF

value: Beating SVF


title: Runx2-input

value: normal culture


title: ESC_B4_H3K4me3_rep2

value: Embryonic Stem Cells


title: Sample_108: DLBCL tissue eRRBS


title: Beating SVF rep2


title: Beating SVF rep1


title: 18A0973

description: RNA extracted from FFPE tissue


title: Runx2-IgG


title: ESC_B4_H3K4me3_rep1


title: 18A0972

description: RNA extracted from FFPE tissue


title: ESC_B15_H3K27me3_rep3

value: ES line B15


title: Runx2-FLAG


title: Sample_107: DLBCL tissue eRRBS


title: Beating SVF rep3


title: 18A0991

description: RNA extracted from FFPE tissue


title: 18A0971

description: RNA extracted from FFPE tissue


title: Sample_106: DLBCL tissue RNA


title: 18A0970

description: RNA extracted from FFPE tissue


title: Sample_105: DLBCL tissue RNA


title: ESC_B4_H3K27me3_rep3


title: Sample_105: DLBCL tissue eRRBS


title: Sample_104: DLBCL tissue eRRBS


title: ESC_B4_H3K27me3_rep2


title: ESC_B15_H3K27me3_rep1


title: 18A0963

description: RNA extracted from FFPE tissue


title: Sample_107: DLBCL tissue RNA


title: Sample_103: DLBCL tissue RNA


title: Sample_103: DLBCL tissue eRRBS


title: 18A0961

description: RNA extracted from FFPE tissue


title: 18A0959

description: RNA extracted from FFPE tissue


title: ESC_B15_H3K27ac_rep3


title: 18A0960

description: RNA extracted from FFPE tissue


title: Sample_102: DLBCL tissue eRRBS


title: ESC_B15_H3K27ac_rep2


title: Sample_101: DLBCL tissue RNA


title: 18A0969

description: RNA extracted from FFPE tissue


title: ESC_B15_H3K27ac_rep1


title: 18A0962

description: RNA extracted from FFPE tissue


title: ESC_B4_H3K27ac_rep3


title: Sample_101: DLBCL tissue eRRBS


title: 18A0942

description: RNA extracted from FFPE tissue


title: ESC_B4_H3K27me3_rep1


title: Sample_100: DLBCL tissue eRRBS


title: 18A0941

description: RNA extracted from FFPE tissue


title: Sample_99: DLBCL tissue RNA


title: ESC_B4_H3K27ac_rep1


title: 18A0943

description: RNA extracted from FFPE tissue


title: 18A0933

description: RNA extracted from FFPE tissue


title: Sample_98: DLBCL tissue RNA


title: 18A0939

description: RNA extracted from FFPE tissue


title: 18A0940

description: RNA extracted from FFPE tissue


title: iPSC_M14939#3_RNAseq_rep3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Baboon RNA-seq reads files were mapping to UCSC papAnu4 by Rsubread with default parameters.
read counts were summarized by featurecounts
DEGs were analyzed by edgeR
Genome_build: papAnu4
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Induced pluripotent stem cells

extract_protocol: RNA-Seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634888, Clontech Laboratories, Moutain View, CA) and the Nextera XT DNA Library Prep Kit (FC-131-1024, Illumina, San Diego, CA) according to the manufacturers’ specifications.

value: iPS line M14939#3


title: Sample_98: DLBCL tissue eRRBS


title: iPSC_M14939#3_RNAseq_rep2_lane1

value: Induced pluripotent stem cells


title: iPSC_M14939#3_RNAseq_rep2_lane2


title: ESC_B4_H3K27ac_rep2


title: Sample_99: DLBCL tissue eRRBS


title: 18A0932

description: RNA extracted from FFPE tissue

source_name: FFPE liver


title: iPSC_M14939#3_RNAseq_rep1


title: 18A0930

description: RNA extracted from FFPE tissue


title: iPSC_160-2_RNAseq_rep3

value: iPS line 160-2


title: Sample_97: DLBCL tissue RNA


title: 18A0929

description: RNA extracted from FFPE tissue


title: Sample_96: DLBCL tissue RNA


title: Sample_94: DLBCL tissue RNA


title: iPSC_160-2_RNAseq_rep1_lane1


title: 18A0912

description: RNA extracted from FFPE tissue


title: 18A0910

description: RNA extracted from FFPE tissue


title: Sample_93: DLBCL tissue RNA


title: Sample_95: DLBCL tissue eRRBS


title: ESC_B15_RNAseq_rep3

source_name: Embryonic Stem Cells


title: iPSC_160-2_RNAseq_rep1_lane2


title: WT 2

city: Solna

first: Martin

last: Rottenberg

address: Solna vägen 9

institute: Karolinska Institutet

hyb_protocol: Fifteen micrograms of biotin-labeled target cRNA was then fragmented and used to prepare a hybridization mixture, which included probe array controls and blocking agents. Hybridization, washing and scanning were performed according to the manufacturers recommendations.

scan_protocol: Affimetrix MTA-1_0

data_processing:
Absolute levels of expression of genes were determined and scaled to 150 using algorithms in MicroArray Analysis suite 5.0 (MAS5) software (Affimetrix).
. In-depth analyses and clustering of data were conducted using GeneSpring software (Silicon Genetics).

source_name: thymic epithelial cell

label_protocol: cDNA was specifically transcribed from 500 ng of mRNA using a Poly-T nucleotide primer containing a T7 RNA polymerase promoter (Geneworks). Biotinylated, antisense target cRNA was subsequently synthesized by in vitro transcription using the BioArray High Yield RNA Transcript Labeling kit (Enzo Diagnostics).

extract_protocol: RNeasy Total RNA Isolation Kit (Qiagen)

treatment_protocol: RNA was extraceted from flow cell  sorted CD45 neg EpcaM pos thymic epithelial cells from mutant and WT mice 7 days after treatment with Tamoxifen


title: 18A0909

description: RNA extracted from FFPE tissue


title: WT 3


title: Sample_93: DLBCL tissue eRRBS


title: ESC_B15_RNAseq_rep2_lane2


title: WT 1


title: KO 3

value: socs3fl/fl act cre ER


title: iPSC_160-2_RNAseq_rep2


title: KO 2


title: ESC_B15_RNAseq_rep2_lane1


title: Sample_92: DLBCL tissue eRRBS


title: 18A0899

description: RNA extracted from FFPE tissue


title: Sample_92: DLBCL tissue RNA


title: Sample_94: DLBCL tissue eRRBS


title: ESC_B15_RNAseq_rep1_lane2


title: Sample_91: DLBCL tissue RNA


title: 18A0913

description: RNA extracted from FFPE tissue


title: methylation_participant 3_Straight (ST)_Post

type: genomic

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

department: Institute for Physical Performance

country: Norway

institute: Norwegian School of Sport Sciences

description:
203265020031_R06C01_green
203265020031_R06C01_red

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using Infinium Methylation NXT setting

data_processing:
Partek Genomic Suite V7 (Using MethylationEPIC_v-1-0_B4 manifest file)
Data is normalised via functional normalisation (with noob background correction)

source_name: DNA from Vastus Lateralis Muscle_Participant 3_Straight (ST)_Post

label_protocol: The DNA was then bisulfite converted using the EZ DNA Methylation Kit, Zymo Research, CA, United States, as per manufacturer’s instructions.

extract_protocol: Genomic DNA was extracted via the Qiagen DNA Easy Kit in accordance with  manufacturers guidelines. T

tag: gender

value: Male

value: Skeletal Muscle_Vastus Lateralis

tag: timepoint

value: Post_30 minutes Post Exercise

tag: health status

value: Young Healthy Adult

tag: experimental condition

value: Straight (ST) Line Running Exercise


title: KO 1


title: 18A0883

description: RNA extracted from FFPE tissue

tag: tissue

value: liver


title: ESC_B15_RNAseq_rep1_lane1


title: methylation_participant 1_Straight (ST)_Post

description:
203265020031_R03C01_green
203265020031_R03C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 1_Straight (ST)_Post


title: methylation_participant 2_Change of Direction (COD)_Baseline

description:
203265020027_R04C01_green
203265020027_R04C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 2_Change of Direction (COD)_Baseline

value: Baseline_rested pre exercise

value: Change of Direction (COD) Running Exercise


title: methylation_participant 3_Change of Direction (COD)_24 h

description:
203265020031_R01C01_green
203265020031_R01C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 3_Change of Direction (COD)_24 h

value: 24 h_24 h Post Exercise


title: ESC_B4_RNAseq_rep3

value: ES line B4


title: methylation_participant 3_Straight (ST)_24 h

description:
203265020031_R07C01_green
203265020031_R07C01_red

source_name: DNA from Vastus Lateralis Muscle Biopsy_Participant 3_Straight (ST)_24 h


title: ESC_B4_RNAseq_rep2_lane2


title: 18A0882

description: RNA extracted from FFPE tissue

tag: treatment

value: wildtype


title: 18A0881

description: RNA extracted from FFPE tissue

tag: strain


title: methylation_participant 2_Straight (ST)_Post

description:
203265020031_R08C01_green
203265020031_R08C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 2_Straight (ST)_Post


title: methylation_participant 2_Straight (ST)_24 h

description:
203265020031_R05C01_green
203265020031_R05C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 2_Straight (ST)_24 h


title: 18A0903

description: RNA extracted from FFPE tissue

tag: time


title: methylation_participant 1_Straight (ST)_Baseline

description:
203265020031_R02C01_green
203265020031_R02C01_red

source_name: DNA from Vastus Lateralis Muscle_Biopsy_Participant 1_Straight (ST)_Baseline


title: 18A0880

description: RNA extracted from FFPE tissue

tag: genotype


title: methylation_participant 3_Change of Direction (COD)_Post

description:
203265020027_R08C01_green
203265020027_R08C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 3_Change of Direction (COD)_Post


title: ESC_B4_RNAseq_rep2_lane1

value: Embryonic Stem Cells


title: methylation_participant 1_Straight (ST)_24 h

description:
203265020031_R04C01_green
203265020031_R04C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 1_Straight (ST)_24 h


title: methylation_participant 3_Change of Direction (COD)_Baseline

description:
203265020027_R07C01_green
203265020027_R07C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 3_Change of Direction (COD)_Baseline


title: Sample_89: DLBCL tissue RNA

source_name: DLBCL tumor sample

value: Diffuse large B-cell lymphoma (DLBCL)


title: Sample_88: DLBCL tissue eRRBS


title: methylation_participant 1_Change of Direction (COD)_24 h

description:
203265020027_R03C01_green
203265020027_R03C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 1_Change of Direction (COD)_24 h


title: ESC_B4_RNAseq_rep1_lane2


title: methylation_participant 1_Change of Direction (COD)_Post

description:
203265020027_R02C01_green
203265020027_R02C01_red

source_name: DNA from Vastus Lateralis Muscle _Participant 1_Change of Direction (COD)_Post


title: 18A0879

description: RNA extracted from FFPE tissue

source_name: FFPE liver


title: Sample_87: DLBCL tissue eRRBS


title: hDSCs_20%O2

city: Ikoma

first: Hitomi

last: Takada

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Science and Technology

institute: Nara Institute of Science and Technology

description: Gene expression in hDSCs cultured under 20%-O2 condition

hyb_protocol: 0.6 ug Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA)  was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Fragmentation buffer and 2x Blocking agent. 25 uL of 2x Hi-RPM Hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE microarray 8360K (G4851A; Agilent Technologies) for 17 hours at 65 °C. After hybridization, the array slides were washed 1 minute with Agilent Gene Expression Wash Buffer1 at room temperature,1 minute with Agilent Gene Expression Wash Buffer 2 at 37°C, 15 seconds with acetonitrile (Wako), and dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid:028004_D_F_20140326 ) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Dermal sheath cells cultured under 20%-O2 condition for four weeks.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling kit (Agilent) according to manufacturer's instructions, followed by Rneasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000c Sepctrophotometer.

extract_protocol: hDPCs cultured under 20%-O2 or 6%-O2 condition were dissolved with Isogen, and total RNA was isolated. Total RNAs of the both group were purified using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations.

treatment_protocol: Human scalp and facial skin with hair were obtained from facelift operations, and DSCs were isolated from hair follicles under microscope. DSCs were cultured in DMEM supplemented with 10% fetal bovine serum and FGF2 (10 ng/mL) for four weeks under 6% O2 or 20% O2 condition.

tag: culture condition

value: 20% oxygen condition


title: ESC_B4_RNAseq_rep1_lane1

source_name: Embryonic Stem Cells


title: hDPCs_6%O2

description: Gene expression in hDPCs cultured under 6%-O2 condition

source_name: Human dermal papillia cells cultured under 6%-O2 condition for four weeks.

extract_protocol: hDPCs cultured under 20%-O2 or 6%-O2 condition were dissolved with Isogen, and total RNA was isolated according to manufacturer's protocol. Total RNAs of the both group were purified using the RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Human scalp and facial skin with hair were obtained from facelift operations, and DPCs were isolated from hair follicles under microscope. DPCs were cultured in keratinocyte conditioned medium for four weeks under 6% O2 or 20% O2 condition.

value: 6% oxygen condition


title: Anti-him-8 piRNAi, rep 2, RNA-seq

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
total RNA, rRNA-depleted, fragmented
rawcounts_genebygene_SG1020_lib15_16_17_18_19_20_21.csv

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: csv text file. The content includes raw counts for each protein coding gene (row)  for each library (column) used in this study.

organism: Caenorhabditis elegans

source_name: Young adult animals

extract_protocol:
RNA extraction was performed using the TRIzol Reagent. Ribosomal RNA (rRNA) was removed from the total RNA using RNase H and anti-rRNA oligo mixture. 1.25 µg of anti-rRNA oligos were mixed with 0.5 µg total RNA in 1x Hybridization Buffer (100 mM Tris-HCl pH 7.4, 200mM NaCl) in a final volume of 8 µl.  The sample was denatured at 95°C for 2 minutes, and then cooled at −0.1 °C /sec to 45°C.  Equal volumes of Hybridase Thermostable RNase H (5U/µl,Epicentre) and 10x RNaseH Reaction Buffer (500 mM Tris-HCl pH 7.4, 1 M NaCl, 200 mM MgCl2) were mixed and preheated to 45°C before use. 2 µl of the enzyme mix was added to each reaction mix, which was then incubated at 45°C for 1 hr. To remove DNA oligos, 5 µl TURBO DNase buffer, 3 µl TURBO DNase (Invitrogen), and 32 µl diH2O were added to the reaction mix, followed by 37˚C incubation for 30 minutes.  To purify RNA, 300 µl STOP solution (1 M ammonium acetate, 10 mM EDTA) was added to the reaction mix, followed by phenol/chloroform (1:1) extraction and ethanol precipitation. RNA was then fragmented using Fragmentation Reagents (Ambion).
RNA-seq libraries were prepared using Takara SMARTer stranded RNA-seq Kits according to the manufacturer's instructions

value: kstEx22 [21ur-1224 anti-him-8 + Pmyo-2::mCherry + Prps-27::hygromycinR]

tag: pirnai target gene

tag: chip antibody

tag: rna-seq method

value: Takara SMARTer Stranded RNA-seq kit

tag: 5’ barcodes for srna or rna-seq


title: Anti-him-8 piRNAi, rep 1, RNA-seq

value: kstEx23 [21ur-1224 anti-him-8 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: 18A0873

description: RNA extracted from FFPE tissue


title: Anti-him-5 piRNAi, rep 2, RNA-seq

value: kstEx20 [21ur-1224 anti-him-5 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: hDPCs_20%O2

description: Gene expression in hDPCs cultured under 20%-O2 condition

source_name: Human dermal papillia cells cultured under 20%-O2 condition for four weeks.


title: Anti-him-5 piRNAi, rep 1, RNA-seq

value: kstEx19 [21ur-1224 anti-him-5 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: cKOUIL-1beta2

data_processing:
BGI
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Primary chondrocytes

extract_protocol:
Primary chondrocytes were isolated as previously described (Gosset M, 2008. Nat Protoc).Total RNA was purified with an RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard BGI protocols

tag: genotype/variation


title: 18A0901

description: RNA extracted from FFPE tissue


title: Sample_86: DLBCL tissue eRRBS


title: methylation_participant 2_Change of Direction (COD)_24 h

description:
203265020027_R06C01_green
203265020027_R06C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 2_Change of Direction (COD)_24 h

value: Male

value: Skeletal Muscle_Vastus Lateralis

value: Young Healthy Adult


title: Multiplex piRNAi, rep 2, RNA-seq

value: kstSi4[Pmex-5::ceGFP::tbb-2; cbr-unc-119(+)] II; unc-119(ed3)III; kstEx30 [21ur-1224 mod_him-5 + 21ur-1224_mod_mCherry + 21ur-1224- anti-ceGFP + 21ur-199 anti-oma-1 + Pmyo-2::mCherry + Prps-27::hygromycinR]

value: him-5, mCherry, GFP, oma-1


title: methylation_participant 1_Change of Direction (COD)_Baseline

description:
203265020027_R01C01_green
203265020027_R01C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 1_Change of Direction (COD)_Baseline

value: Baseline_rested pre exercise

value: Change of Direction (COD) Running Exercise


title: Multiplex piRNAi, rep 1, RNA-seq

value: kstSi4[Pmex-5::ceGFP::tbb-2; cbr-unc-119(+)] II; unc-119(ed3)III; kstEx29 [21ur-1224 mod_him-5 + 21ur-1224_mod_mCherry + 21ur-1224- anti-ceGFP + 21ur-199 anti-oma-1 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: Sample_85: DLBCL tissue RNA


title: 18A0871

description: RNA extracted from FFPE tissue

value: liver

value: wildtype


title: 18A0872

description: RNA extracted from FFPE tissue


title: cKOUIL-1beta1


title: 18A0870

description: RNA extracted from FFPE tissue


title: 18A0869

description: RNA extracted from FFPE tissue


title: methylation_participant 2_Change of Direction (COD)_Post

description:
203265020027_R05C01_green
203265020027_R05C01_red

source_name: DNA from Vastus Lateralis Muscle_Participant 2_Change of Direction (COD)_Post

value: Post_30 minutes Post Exercise


title: Sample_85: DLBCL tissue eRRBS

value: Diffuse large B-cell lymphoma (DLBCL)


title: Sample_84: DLBCL tissue eRRBS


title: CntlIL-1beta2


title: Negative control for multiplex piRNAi, RNA-seq

value: kstSi4[Pmex-5::ceGFP::tbb-2; cbr-unc-119(+)] II; unc-119(ed3)III; kstEx28 [21ur-199 anti-random DNA + Pmyo-2::mCherry + Prps-27::hygromycinR]

value: random DNA


title: Sample_83: DLBCL tissue eRRBS


title: CntlIL-1beta1


title: cKO2


title: Sample_83: DLBCL tissue RNA


title: 18A0853

description: RNA extracted from FFPE tissue


title: Anti-him-8 piRNAi, rep 2, 5’mono-Pi dependent sRNA-seq

description:
total small RNA
piRNA_analysis_report_21U1224_100120a01.csv

extract_protocol:
small RNA was extracted by using mirVana™ miRNA Isolation Kit (ThermoFisher).
Small RNA-seq was performed using a 5’-monophosphate-dependent small RNA cloning procedure described in Gent, J.I. et al. A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Genetics 183, 1297–1314 (2009).

value: kstEx22 [21ur-1224 anti-him-8 + Pmyo-2::mCherry + Prps-27::hygromycinR]

value: Ligation-based sRNA-seq, 5’-linker ligation is dependent of the 5’-mono phosphate of the small RNAs

value: mixture of AGCG, CGTC, GTTA, and TATG


title: Anti-him-8 piRNAi, rep 1, 5’mono-Pi dependent sRNA-seq

value: kstEx23 [21ur-1224 anti-him-8 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: cKO1


title: 18A0852

description: RNA extracted from FFPE tissue


title: Sample_82: DLBCL tissue RNA


title: Cntl2


title: Cntl1


title: Anti-him-5 piRNAi, rep 1, 5’mono-Pi dependent sRNA-seq

value: kstEx19 [21ur-1224 anti-him-5 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: Anti-him-5 piRNAi, rep 2, 5’mono-Pi dependent sRNA-seq

value: kstEx20 [21ur-1224 anti-him-5 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: Sample_81: DLBCL tissue RNA


title: 18A0851

description: RNA extracted from FFPE tissue


title: 18A0850

description: RNA extracted from FFPE tissue


title: Sample_82: DLBCL tissue eRRBS


title: Sample_80: DLBCL tissue RNA


title: Negative control for multiplex piRNAi, 5’mono-Pi dependent sRNA-seq


title: Mock Infection Native ChIP- Protein VII IP

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Cells contain protein VII induction plasmid (DA0203)

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v3.4.4 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20.
ChIP-seq reads were aligned to human genome hg38 and yeast genome sacCer3 separately using Bowtie2.3.4.3 with following options: -p --no-discordant --no-mixed.
Peaks in H3 and VII with respect to ChIP input in the yeast genome were called using MACS2 callpeak function in narrow peak mode with the following options: -f BAMPE -g 12100000 --bdg --keep-dup 1 -q 0.05
Genome_build: hg38; sacCer3
Supplementary_files_format_and_content: bedGraph files produced by MACS2 callpeak --bdg
Supplementary_files_format_and_content: narrowPeak files produced by MACS2

organism:
Saccharomyces cerevisiae
Homo sapiens

source_name: Native chromatin: human with S. cerevisiae spike-in

growth_protocol: Human cells were grown in EMEM with 10% FBS + 1% penicillin and streptomycin. Yeast were pre-grown in selection media lacking uracil with 2% raffinose.

extract_protocol:
Human chromatin was purified by cell lysis, MNase digest, and ultrasonic liquid sonication in a custom ChIP buffer for protein VII purification. Yeast native chromatin was purified from cells and ChIP performed as in PMID: 23468649.
Libraries were prepared from the ChIP samples as well as a 10% input, following manufacturer recommendations, with KAPA Biosystems Unique Dual-Indexed Adapter Kit (#KK8727), Hyper Prep Kit (#KK8504), and Beckman Coulter AMPure XP Beads (#A63880) for library cleanup and size selection. Library concentrations were measured with Invitrogen Qubit dsDNA HS Assay Kit (#Q32851), then analyzed with Agilent High Sensitivity D5000 ScreenTape System, and pooled. Libraries were sequenced with 50-bp paired-end reads using SP Flow Cell on an Illumina NovaSeq 6000 sequencer at the Fred Hutch Genomics Core Facility.

treatment_protocol: Human cells were grown to 90% confluence, then mock infected and harvested 20 hours later. Yeast were induced to express adenovirus protein VII by adding 2% galactose for 4 hours before purifying nuclei.

tag: human cell type

value: IMR 90

tag: yeast strain

value: Adenovirus protein VII (custom anti-VII raised in mouse; publushed in PMID:26332038)

value: Human cells:mock infection at 20 hours; Yeast:4 hours galactose induction


title: Mock Infection Native ChIP- Total H3 IP

extract_protocol:
Human chromatin was purified by cell lysis, MNase digest, and ultrasonic liquid sonication in a custom ChIP buffer for protein VII purification. Yeast native chromatin was purified from cells and ChIP performed as in PMID: 23468649.
Libraries were prepared from the ChIP samples as well as a 10% input, following manufacturer recommendations, with KAPA Biosystems Unique Dual-Indexed Adapter Kit (#KK8727), Hyper Prep Kit (#KK8504), and Beckman Coulter AMPure XP Beads (#A63880) for library cleanup and size selection. Library concentrations were measured with Invitrogen Qubit dsDNA HS Assay Kit (#Q32851), then analyzed with Agilent High Sensitivity D5000 ScreenTape System, and pooled. Libraries were sequenced with 50-bp paired-end reads using SP Flow Cell on an Illumina NovaSeq 6000 Sequencer at the Fred Hutch Genomics Core Facility.

value: Total H3 (abcam, #1791)


title: 18A0842

description: RNA extracted from FFPE tissue

extract_protocol:
Formalin-fixed, paraffin-embedded liver tissue was scraped from sections mounted to glass slides directly into lysis buffer.
The TempO-Seq (BioSpyder Technologies) RNA sequencing protocol was followed for library construction: mRNA targets were hybridized with a detector oligomer probe mix, excess oligos are removed, followed by detector oligo ligation.


title: Sample_80: DLBCL tissue eRRBS


title: Mock Infection Native ChIP- input sample

extract_protocol:
Human chromatin was purified by cell lysis, MNase digest, and ultrasonic liquid sonication in a custom ChIP buffer for protein VII purification. Yeast native chromatin was purified from cells and ChIP performed as in PMID: 23468649.
Libraries were prepared from the ChIP samples as well as a 10% input, following manufacturer recommendations, with KAPA Biosystems Unique Dual-Indexed Adapter Kit (#KK8727), Hyper Prep Kit (#KK8504), and Beckman Coulter AMPure XP Beads (#A63880) for library cleanup and size selection. Library concentrations were measured with Invitrogen Qubit dsDNA HS Assay Kit (#Q32851), then analyzed with Agilent High Sensitivity D5000 ScreenTape System, and pooled. Libraries were sequenced with 50-bp paired-end reads using SP flow cell on an Illumina NovaSeq 6000 sequencer at the Fred Hutch Genomics Core Facility.


title: Sample_79: DLBCL tissue RNA


title: Anti-him-8 piRNAi, rep 2, 5’mono-Pi independent sRNA-seq

description:
total small RNA
rawcounts_genebygene_SG1020_lib1_2_3_4_5_6_7.csv

extract_protocol:
small RNA was extracted by using mirVana™ miRNA Isolation Kit (ThermoFisher).
Small RNA-seq was performed using a 5’-monophosphate-independent small RNA cloning procedure described in Gent, J.I. et al. A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference. Genetics 183, 1297–1314 (2009).

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs


title: 18A0841

description: RNA extracted from FFPE tissue

value: liver


title: Anti-him-8 piRNAi, rep 1, 5’mono-Pi independent sRNA-seq


title: Multiplex piRNAi, rep 2, 5’mono-Pi dependent sRNA-seq

value: kstSi4[Pmex-5::ceGFP::tbb-2; cbr-unc-119(+)] II; unc-119(ed3)III; kstEx30 [21ur-1224 mod_him-5 + 21ur-1224_mod_mCherry + 21ur-1224- anti-ceGFP + 21ur-199 anti-oma-1 + Pmyo-2::mCherry + Prps-27::hygromycinR]

value: him-5, mCherry, GFP, oma-1


title: Sample_78: DLBCL tissue RNA

value: Diffuse large B-cell lymphoma (DLBCL)


title: 18A0849

description: RNA extracted from FFPE tissue

value: wildtype


title: Sample_78: DLBCL tissue eRRBS


title: Multiplex piRNAi, rep 1, 5’mono-Pi dependent sRNA-seq

value: kstSi4[Pmex-5::ceGFP::tbb-2; cbr-unc-119(+)] II; unc-119(ed3)III; kstEx29 [21ur-1224 mod_him-5 + 21ur-1224_mod_mCherry + 21ur-1224- anti-ceGFP + 21ur-199 anti-oma-1 + Pmyo-2::mCherry + Prps-27::hygromycinR]


title: Anti-him-5 piRNAi, rep 1, 5’mono-Pi independent sRNA-seq


title: Anti-him-5 piRNAi, rep 2, 5’mono-Pi independent sRNA-seq


title: Sample_77: DLBCL tissue eRRBS


title: 18A0840

description: RNA extracted from FFPE tissue


title: 18A0839

description: RNA extracted from FFPE tissue


title: 18A0843

description: RNA extracted from FFPE tissue


title: tAN-CR3

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

data_processing:
The quality of the reads was verified using FASTQC version 0.11.5
Viral contamination was removed by aligning the generated reads to a selection of 19 bee virus genomes (GenBank accessions: NC_002548.1, KY354230.1, KY354236.1, KY354237.1, KY354239.1, KY354238.1, KY354240.1, NC_027631.1, NC_003784.1, NC_010711.1, NC_004830.2, KT733632.1, KT733627.1, KT733619.1, NC_009025.1, AB070959.1, AB245506.1, KT733624.1, AB251935.1, NC_004807.1) using STAR 2.5.0a (Dobin et al. 2013, doi: 10.1093/bioinformatics/bts635), and retaining the unmapped (bee virus filtered) reads for subsequent analyses.
All bee virus filtered reads were aligned to the V. destructor genome (Vdes_3.0, GenBank accession GCA_002443255.1) using STAR version 2.5.0a (Dobin et al. 2013, doi: 10.1093/bioinformatics/bts635) with a 2-pass mode, a maximum intron size (--alignIntronMax) of 20 kb and with --sjdbOverhang 124.
Next, read counts per gene were obtained using the htseq-count script included in the HTSeq package (Anders et al. 2015, doi: 10.1093/bioinformatics/btu638) with the following settings "-f bam -r pos -s reverse -i gene -t exon" and a GFF3 annotation file (GCF_002443255.1_Vdes_3.0_genomic_PCG_no_pseudo.gff, version of October 2017, restricted to protein coding genes (10247 nuclear and 13 mitochondrial protein coding genes))
Genome_build: Vdes_3.0, GenBank accession GCA_002443255.1
Supplementary_files_format_and_content: Tab-delimited text including raw read counts (HTSeq) per V. destructor gene ID for each sample

molecule: polyA RNA

organism: Varroa destructor

source_name: complete organism

growth_protocol: Varroa mites were collected from Apis mellifera colonies in Greece. One Varroa population (AN-CR) was collected from an A. mellifera colony on the Aegean island of Andros, where coumaphos had been used almost exclusively for the last 14 years and indications of control failure had been reported by local beekeeper, and another Varroa population (ATH-S) was collected from an A. mellifera colony at the Agricultural University of Athens, retained without chemical treatments for the last 19 years. For each bee colony, bee brood cells were uncapped and Varroa mites that were either on the bee larvae or in the inner surface of the bee brood cell were collected in an Eppendorf tube using a fine paintbrush.

extract_protocol:
Total RNA was extracted from 10-20 adult females from each population/treatment (AN-CR, ATH-S and tAN-CR), with four-fold biological replication for each population/treatment, using the TRI reagent protocol (Invitrogen) following the manufacturer’s instructions. RNA was treated with TURBO™ DNase I (ThermoFisher Scientific) to remove genomic DNA contamination.
Illumina libraries were constructed from the RNA samples with the TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina, USA)
RNAseq libraries were sequenced on an Illumina HiSeq 2500 to generate strand-specific paired reads of 2 x 125 bp (library construction and sequencing was performed at the Genomics Core Facility of the University of Utah, Utah, USA)

treatment_protocol: After collection of Varroa mites from the bee colony, adult female Varroa mites were introduced in glass vials of 12 mL  (10 mites/vial) coated with either acetone (ATH-S and AN-CR) or 200 mg a.i. coumaphos/L acetone (tAN-CR) and kept at 25°C for 20h. Glass vials were coated by adding 500 microL of acetone (ATH-S and AN-CR) or 500 microL of 200 mg a.i. coumaphos/L acetone (tAN-CR)  and rolling vials until acetone evaporated. After 20h, alive mites were collected in an eppendorf tube (20 mites/tube), snap frozen with liquid nitrogen and stored at -80°c until RNA extraction.

tag: Stage

value: female adult

tag: phenotype

value: coumaphos resistant

value: 20h at 25°C in glass vial (12 mL) coated with 500 microL of 200 mg a.i. coumaphos/L acetone


title: Sample_76: DLBCL tissue RNA

extract_protocol: trizol extraction and TruSeq RNA sample prep kit.


title: Multiplex piRNAi, rep 2, 5’mono-Pi independent sRNA-seq

value: mixture of AGCG, CGTC, GTTA, and TATG


title: tAN-CR2


title: tAN-CR1


title: AN-CR3

value: 20h at 25°C in glass vial (12 mL) coated with 500 microL acetone


title: Sample_75: DLBCL tissue eRRBS

extract_protocol: enhanced reduced representation bisulfite sequencing method (eRRBs) was followed as reported in Garrett-Bakelman et al 2015 doi: 10.3791/52246


title: tAN-CR4


title: Multiplex piRNAi, rep 1, 5’mono-Pi independent sRNA-seq


title: Sample_76: DLBCL tissue eRRBS


title: Sample_90: DLBCL tissue RNA


title: Negative control for multiplex piRNAi, 5’mono-Pi independent sRNA-seq

value: kstSi4[Pmex-5::ceGFP::tbb-2; cbr-unc-119(+)] II; unc-119(ed3)III; kstEx28 [21ur-199 anti-random DNA + Pmyo-2::mCherry + Prps-27::hygromycinR]

value: random DNA


title: Sample_74: DLBCL tissue RNA


title: Anti-oma-1 piRNAi, rep 2, 5’mono-Pi dependent sRNA-seq

description:
total small RNA
piRNA_analysis_report_21U199_011921a01.csv

value: Ligation-based sRNA-seq, 5’-linker ligation is dependent of the 5’-mono phosphate of the small RNAs

value: mixture of CTGG, ACTG, GAAG, and TGCC


title: Anti-oma-1 piRNAi, rep 1, 5’mono-Pi dependent sRNA-seq


title: Sample_90: DLBCL tissue eRRBS


title: AN-CR2


title: hDSCs_6%O2

source_name: Dermal sheath cells cultured under 6%-O2 condition for four weeks.

value: 6% oxygen condition


title: Sample_74: DLBCL tissue eRRBS


title: AN-CR1


title: AN-CR4


title: Sample_73: DLBCL tissue RNA


title: ATH-S3

value: coumaphos susceptible


title: ATH-S4


title: ATH-S2


title: Anti-unc-119 piRNAi, rep 2, 5’mono-Pi dependent sRNA-seq


title: Anti-oma-1 piRNAi, rep 2, 5’mono-Pi independent sRNA-seq

description:
total small RNA
rawcounts_genebygene_SG0919_lib25_26_27_28.csv

value: Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs


title: Anti-unc-119 piRNAi, rep 1, 5’mono-Pi dependent sRNA-seq


title: Sample_71: DLBCL tissue eRRBS


title: Sample_71: DLBCL tissue RNA


title: Anti-unc-119 piRNAi, rep 2, 5’mono-Pi independent sRNA-seq


title: FK-L3-4

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

data_processing:
High-throughput sequencing was performed on the llumina NovaSeq .
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
quality filtered reads were mapped to the rabbit reference genome using Salmon 0.14.1
Genome_build: oryCun2
Supplementary_files_format_and_content: comma-delimited csv files include Raw reads counts of each Sample ...

organism: Oryctolagus cuniculus

source_name: rabbits liver tissue

extract_protocol:
The livers of treated rabbits' were trypsinized and collected, and total mRNA was extracted using TRIzol reagent
The TruSeq RNA Sample Preparation kit (Illumina) was used to construct RNA-seq libraries

value: liver

tag: disease state

value: rabbit model of hereditary tyrosinemia type I (HT1)


title: Anti-oma-1 piRNAi, rep 1, 5’mono-Pi independent sRNA-seq


title: ATH-S1


title: Sample_70: DLBCL tissue RNA

source_name: DLBCL tumor sample

value: Diffuse large B-cell lymphoma (DLBCL)


title: Anti-unc-119 piRNAi, rep 1, 5’mono-Pi independent sRNA-seq


title: FK-L3-2


title: FK-L3-3


title: Sample_69: DLBCL tissue RNA


title: 16: TCDD-Infected3_RNAseq

city: Rochester

first: B. Paige

last: Lawrence

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, Unique "-s 0 -t exon -g gene_name"
Genome_build: GRCm38.p5 + Gencode-M12 Annotation
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: TCDD-Infected

extract_protocol:
Peripheral lymph nodes (cervical, axillary, brachial, inguinal, and sacral) were harvested from naïve adult developmentally exposed mice. Mediastinal lymph nodes were harvested from adult developmentally exposed mice on day 9 post IAV infection. Lymph nodes were processed to single cell suspensions, and CD4+ T cells were purified to >90% purity using the MojoSort Mouse CD4+ T cell negative selection isolation kit protocol (BioLegend, San Diego, CA). RNA was isolated from total CD4+ T cells using the RNeasy Mini kit (Qiagen, Valencia, CA). Total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
RNA (1 ng) was pre-amplified with the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, Mountain View, CA) following the manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Fluorometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). For total CD4+ T cells, 150 pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell, and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 10 pM per lane. Single end reads of 100nt were generated for each sample using Illumina's HiSeq2500v4.

treatment_protocol: Impregnated and lactating dams were gavaged with vehicle (peanut oil) or 1ug 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)/kg body weight on gestational day 0, 7, 14, and post natal day 2. Offspring were aged to maturity (6-10 weeks old), and CD4+ T cells were purified from naive mice or mice infected with 120 HAU Influenza A virus (HKx31).

value: CD4+ T cells


title: FK-L3-1


title: Anti-oma-1 piRNAi, rep 2, RNA-seq

description:
total RNA, rRNA-depleted, fragmented
rawcounts_genebygene_SG0919_lib19_20_21_22.csv

extract_protocol:
RNA extraction was performed using the TRIzol Reagent. Ribosomal RNA (rRNA) was removed from the total RNA using RNase H and anti-rRNA oligo mixture. 1.25 µg of anti-rRNA oligos were mixed with 0.5 µg total RNA in 1x Hybridization Buffer (100 mM Tris-HCl pH 7.4, 200mM NaCl) in a final volume of 8 µl.  The sample was denatured at 95°C for 2 minutes, and then cooled at −0.1 °C /sec to 45°C.  Equal volumes of Hybridase Thermostable RNase H (5U/µl,Epicentre) and 10x RNaseH Reaction Buffer (500 mM Tris-HCl pH 7.4, 1 M NaCl, 200 mM MgCl2) were mixed and preheated to 45°C before use. 2 µl of the enzyme mix was added to each reaction mix, which was then incubated at 45°C for 1 hr. To remove DNA oligos, 5 µl TURBO DNase buffer, 3 µl TURBO DNase (Invitrogen), and 32 µl diH2O were added to the reaction mix, followed by 37˚C incubation for 30 minutes.  To purify RNA, 300 µl STOP solution (1 M ammonium acetate, 10 mM EDTA) was added to the reaction mix, followed by phenol/chloroform (1:1) extraction and ethanol precipitation. RNA was then fragmented using Fragmentation Reagents (Ambion).
RNA-seq library was prepared using the protocol described in Ni. et. al. 2014 (PMID: 25534009)

value: Ligation-based RNA-seq


title: Sample_69: DLBCL tissue eRRBS


title: FK-L2-4


title: 14: TCDD-Infected2_RNAseq


title: Anti-oma-1 piRNAi, rep 1, RNA-seq


title: Sample_68: DLBCL tissue eRRBS


title: Anti-unc-119 piRNAi, rep 2, RNA-seq


title: 15: Vehicle-Infected3_RNAseq

source_name: Vehicle-Infected


title: Sample_68: DLBCL tissue RNA


title: Sample_67: DLBCL tissue RNA


title: FK-L2-2


title: Anti-unc-119 piRNAi, rep 1, RNA-seq


title: FK-L2-3


title: 10: TCDD-Infected1_RNAseq


title: 13: Vehicle-Infected2_RNAseq


title: Sample_66: DLBCL tissue eRRBS


title: 9: Vehicle-Infected1_RNAseq


title: FK-L2-1


title: Anti-oma-1 piRNAi, rep 1,  H3K9me3 ChIP-seq

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0919_lib1_to_12.csv

extract_protocol:
110-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions

value: Abcam, ab8898, anti-H3K9me3


title: Sample_65: DLBCL tissue eRRBS


title: FK-L1-4


title: Anti-oma-1 piRNAi, rep 2,  H3K9me3 ChIP-seq

extract_protocol:
111-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: Sample_64: DLBCL tissue RNA


title: FK-L1-3


title: Anti-unc-119 piRNAi, rep 2,  H3K9me3 ChIP-seq

extract_protocol:
109-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: 8: TCDD-Naive3_RNAseq

source_name: TCDD-Naive


title: 7: Vehicle-Naive3_RNAseq

source_name: Vehicle-Naive


title: Sample_64: DLBCL tissue eRRBS


title: FK-L1-2


title: 6: TCDD-Naive2_RNAseq


title: 5: Vehicle-Naive2_RNAseq


title: Sample_63: DLBCL tissue eRRBS


title: Anti-oma-1 piRNAi, rep 1,  Pol II (S2) ChIP-seq

extract_protocol:
106-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions

value: Abcam, ab5095, Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody


title: Anti-oma-1 piRNAi, rep 2,  Pol II (S2) ChIP-seq

extract_protocol:
107-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: Sample_72: DLBCL tissue eRRBS


title: Anti-unc-119 piRNAi, rep 1, H3K9me3 ChIP-seq

extract_protocol:
108-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: Anti-unc-119 piRNAi, rep 2,  Pol II (S2) ChIP-seq

extract_protocol:
105-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: FA3-L-3


title: Sample_61: DLBCL tissue RNA


title: Sample_62: DLBCL tissue eRRBS


title: Anti-unc-119 piRNAi, rep 1, Pol II (S2) ChIP-seq

extract_protocol:
104-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: 2: TCDD-Naive1_RNAseq


title: 1: Vehicle-Naive1_RNAseq

extract_protocol: Peripheral lymph nodes (cervical, axillary, brachial, inguinal, and sacral) were harvested from naïve adult developmentally exposed mice. Mediastinal lymph nodes were harvested from adult developmentally exposed mice on day 9 post IAV infection. Lymph nodes were processed to single cell suspensions, and CD4+ T cells were purified to >90% purity using the MojoSort Mouse CD4+ T cell negative selection isolation kit protocol (BioLegend, San Diego, CA). RNA was isolated from total CD4+ T cells using the RNeasy Mini kit (Qiagen, Valencia, CA). Total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).


title: 16: TCDD-Infected3_WGBS

data_processing:
bcltofastq-2.19.0
trim_galore-0.4.3, "--paired --clip_r1 8 --clip_r2 8 --three_prime_clip_r1 8 --three_prime_clip_r2 8"
bismark-0.18.1, bismark "--bowtie2 --maxins 1000 --multicore 3"
bismark-0.18.1, filter_non_conversion
bismark-0.18.1, deduplicate_bismark
smtools-1.4.1, sort
MethylKit-1.4.0, processBismarkAln "save.context="CpG",read.context="CpG",nolap=TRUE,mincov=2,minqual=10,phred64=FALSE"
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited, MethylKit CpG extracted data

extract_protocol:
Peripheral lymph nodes (cervical, axillary, brachial, inguinal, and sacral) were harvested from naïve adult developmentally exposed mice. Mediastinal lymph nodes were harvested from adult developmentally exposed mice on day 9 post IAV infection. Lymph nodes were processed to single cell suspensions, and CD4+ T cells were purified to >90% purity using the MojoSort Mouse CD4+ T cell negative selection isolation kit protocol (BioLegend, San Diego, CA). DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Valencia, CA), and then processed for whole genome bisulfite sequencing. Genomic DNA was quantified using the Qubit fluorometer (Life Technologies, Grand Island, NY). DNA integrity was determined using the TapeStation with genomics DNA tape reagents (Agilent, Santa Clara, CA).
Methylation libraries were generated with Illumina’s TruSeq DNA Methylation Kit.Briefly, bisulfite conversion was carried out on 100 ng of genomics DNA using Zymo EZ DNA Methylation Gold per manufacturer’s recommendations (Zymo Research, Irvine, CA) and conversion efficiency was determined with the Bioanalyzer 2100 (Agilent, Santa Clara, CA). Single-stranded cDNA was generated and tagged from Bisulfite converted DNA using random hexamers containing a 5` tag followed by terminal tagging to mark the 3` end of the DNA. Illumina specific adaptors were added during PCR amplification. DNA libraries were purified with AmpureXP beads and quantified with Bioanalyzer 2100 and Qubit fluorometer. The amplified libraries were hybridized to the Illumina pair end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Pair end reads of 126nt were generated on the Illumina HiSeq2500 for each sample.

value: CD4+  T cells


title: Anti-oma-1 piRNAi, rep 2, ChIP input

extract_protocol:
103-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: FA3-L-1


title: Anti-oma-1 piRNAi, rep 1, ChIP input

extract_protocol:
102-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions