title: PIT_P5-PIT_P6-D10-AD001


title: Kcr CHIP of endoderm cells [YFH7]

status: Public on Feb 23 2021

type: SRA

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

country: USA

institute: NIEHS

library_source: genomic

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
For each sample, raw reads from re-sequencing were pooled together. Pooled raw reads were filtered based on a mean base quality score > 20, and adapters were trimmed by “trim_galore” (version 0.4). Trimmed reads were mapped to hg19 using Bowtie1 with the parameters “-m1, -v2 --best --strata -X 1500”. For each condition/treatment, aligned read files from replicate samples were merged together using function merge from samtools (Version 1.3.1). For all merged files, duplicates were removed using Picard (Version 1.115).
We used program called findPeaks from Homer (Version 4.8.3) to call all reported ChIP-seq peaks. The basic idea is to identify regions in the genome where we find more sequencing reads than we would expect to see by chance. Peak calling for all samples used pooled input sample as noise control. findPeaks was run default parameters, with “-F 2 -L 0 -C 1.5 -fdr 0.001”.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bedgraph files using bedGraphToBigWig.

molecule: genomic DNA

organism: Homo sapiens

source_name: ES derived endoderm cells

growth_protocol: Human embryonic stem cells were cultured with TesR-E8 medium in Matrigel -coated plates. Endoderm cells were induced by endoderm differentiation kit (StemCell Technologies) for 3 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: induced endoderm cells

tag: chip antibody

value: Pan anti-crotonyllysine rabbit antibody (PTM biolabs., PTM 501)


title: PIT_P1-PIT_P2-A1-AD004

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6 Male, brain dissected in P56

extract_protocol:
The snmC-seq2 protocol was applied to individual nuclei isolated from pituitary pooled from 30 adult male C57BL/6 mice
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: tissue

value: Pituitary

tag: age

tag: strain

tag: Sex

value: male


title: CD5naiBC_G02

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: single cell RRBS

data_processing:
Bulk RRBS processing: Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.05 -s 16 -w 100 -S 1 -R -u -m 0. Methylation rates were called using custom scripts and subsequently filtered for coverage (min 10).
Single cell processing: Adapter clipping and quality trimming using cutadapt. Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.1 -s 12 -q 20 -w 100 -S 1 -R -u -m 0. Methylation rates were called using mcall.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file from coverage filtered Bed file (<chr> <start> <end> <methylation rate>)

source_name: blood

extract_protocol:
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.

tag: patient id

value: HD

tag: diagnosis

value: CD5+ naive B cell

tag: ighv

tag: treatmentstatus


title: Kcr CHIP of endoderm cells [YFH6]


title: CD5naiBC_F06

description: single cell RRBS


title: PIT_P5-PIT_P6-A3-AD010


title: Kcr CHIP of ES cells [YFH5]

source_name: ES cells


title: H3K27ac CHIP of ES cells [YFH9]

value: anti-H3K27ac (abcam, ab177178)


title: PIT_P1-PIT_P2-B11-AD002


title: CD5naiBC_F05

description: single cell RRBS


title: CD5naiBC_F04

description: single cell RRBS


title: PIT_P7-PIT_P8-H2-AD006


title: PIT_P5-PIT_P6-H12-AD006


title: PIT_P5-PIT_P6-G12-AD001


title: Kcr CHIP of ES cells [YFH3]


title: PIT_P1-PIT_P2-A4-AD002


title: PIT_P3-PIT_P4-D1-AD012


title: PIT_P5-PIT_P6-F12-AD010


title: CD5naiBC_G03

description: single cell RRBS


title: PIT_P7-PIT_P8-A3-AD001


title: CD5naiBC_F03

description: single cell RRBS


title: CD5naiBC_F02

description: single cell RRBS


title: PIT_P1-PIT_P2-F11-AD012


title: PIT_P5-PIT_P6-B4-AD004


title: ES cell input [YFH1]


title: PIT_P5-PIT_P6-A10-AD010


title: CD5naiBC_F01

description: single cell RRBS


title: PIT_P3-PIT_P4-E2-AD012


title: endoderm cells with acetate

library_source: transcriptomic

data_processing:
Constructed libraries were sequenced on a NextSeq 500 Illumina platform, producing 68nt+75nt stranded paired end reads. Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Reads were parsed for cell barcode and UMI information, filtering out reads according to the following constraints: no 6nt barcode segment is more than a Hamming distance of 1 from a valid barcode block; all linker segments are within 1nt length of the expected value; the UMI has a length of 8nt; and only 1 mismatch is allowed within the ACG-GAC segments flanking the UMI.
Reads were mapped to hg19 using STAR with the UCSC refSeq (Downloaded from UCSC August 18th, 2017) annotation. Gene assignments were carried out using subread featureCounts version 1.6.3 using this same annotation prior to PCR deduplication and count accumulation using umi_tools version 0.5.0, allowing for a single edit for UMI matching.
Valid cell barcodes were identified using DropletUtils R package (version 1.2.2).
Genome_build: hg19
Supplementary_files_format_and_content: feature-barcode matrix which contains only detected cellular barcords.

molecule: polyA RNA

source_name: differentiated cells

growth_protocol: Human embryonic stem cells were cultured with TesR-E8 medium in Matrigel-coated plates. Endoderm cells were induced by endoderm differentiation kit from Stemcell Technologies.

extract_protocol:
Single cells were individually partitioned into subnanoliter droplets on a cartridge using a one-touch ddSEQ Single-Cell Isolator. Cell lysis and cell barcoding occur inside individual droplets, and single-cell-barcoded RNA-Seq libraries are subsequently prepared using Nextera technology.
SureCell WTA 3′ Library Prep Kit for the ddSEQ System.

treatment_protocol: Human embryonic stem cells were induced for endoderm cells for 3 days in the absence or presence of crotonate or acetate.

value: endoderm cells induced with acetate

tag: genotype

value: WT


title: PIT_P3-PIT_P4-G2-AD012


title: PIT_P7-PIT_P8-F7-AD001


title: PIT_P7-PIT_P8-H7-AD001


title: endoderm cells with crotonate

value: endoderm cells induced with crotonate


title: PIT_P5-PIT_P6-C9-AD002


title: CD5naiBC_E04

description: single cell RRBS


title: CD5naiBC_E06

description: single cell RRBS


title: PIT_P5-PIT_P6-F2-AD004


title: PIT_P1-PIT_P2-D10-AD012


title: Kcr CHIP of ES cells [YFH4]


title: differentiated cell input [YFH2]


title: ES cells


title: PIT_P3-PIT_P4-C12-AD008


title: PIT_P1-PIT_P2-F12-AD007


title: PIT_P7-PIT_P8-E9-AD002


title: endoderm cells 2

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
Reads were filtered based on a mean base quality score > 20, and adapters were trimmed by “trim_galore” (version 0.4). Trimmed reads were mapped to hg19 using STAR aligner (version 2.6) separately. Subread featureCounts (version 1.4.6) was applied for gene quantification based on UCSC hg19 RefSeq gene release (downloaded August 18th, 2017).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count or log2 transformed DESeq2 normalized counts for each sample

molecule: total RNA

growth_protocol: Human Embryonic Stem Cells were cultured with TesR-E8 medium (Stemcell Techologies) in Matrigel-coated plates. Endoderm cells were induced by the endoderm differentiation kit (STEMdiff Trilineage Differentiation kit, Stemcell Technologies)

extract_protocol:
RNA was extracted by RNeasy miniprep kit (Qiagen).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.


title: CD5naiBC_E02

description: single cell RRBS


title: CD5naiBC_D05

description: single cell RRBS


title: endoderm cells


title: endoderm cells 3


title: CD5naiBC_E01

description: single cell RRBS


title: PIT_P3-PIT_P4-B11-AD010


title: PIT_P1-PIT_P2-C1-AD010


title: PIT_P7-PIT_P8-B2-AD002


title: endoderm cells 1


title: CD5naiBC_D04

description: single cell RRBS


title: PIT_P5-PIT_P6-D1-AD012


title: ES cells 3


title: PIT_P3-PIT_P4-H9-AD001


title: CD5naiBC_E03

description: single cell RRBS


title: ES cells 2


title: CD5naiBC_D03

description: single cell RRBS


title: PIT_P3-PIT_P4-H1-AD006


title: CD5naiBC_D02

description: single cell RRBS


title: PIT_P3-PIT_P4-A4-AD010


title: OT-I RNA-seq 60 min. unstimulated rep3

city: Aurora

first: Leslie

last: Berg

state: Colorado

address: 12800 East 19th Avenue MS 8333, RC1 North room P18-8101

department: Immunology and Microbiology Department

institute: University of Colorado School of Medicine

data_processing:
Adapter sequences were trimmed from quality raw sequencing reads with Trimmomatic-0.38 (Bolger et al., 2014).
Reads were aligned to mouse ribosomal RNA with Bowtie2 v2.3.2 (Langmead and Salzberg, 2012).
Non-ribosomal reads were retained, and aligned to a mm10 RefSeq transcriptome with Bowtie2 v2.3.2.
Gene expression was estimated (transcripts per million and expected counts) with RSEM v1.2.29 (Li and Dewey, 2011)
Genome_build: mm10
Supplementary_files_format_and_content: RSEM expected counts of three replicate experiments were grouped into a DESeq2 dataset for differential expression analysis with DESeq2 v1.26.0 (Love et al., 2014). Also provided are RSEM TPM matrices for each replicate.

source_name: CD8+ OT-I T cells

extract_protocol:
Samples of stimulated CD45.2+ OT-I cells and CD45.1+ wildtype splenocytes mixtures were stained with CD8a and CD45.2 antibodies and 7-AAD and OT-I cells were sorted (BD FACSAria) into 100% FBS and pelleted. Total RNA from ~300,000 OT-I cells per sample was collected with the RNeasy micro kit (Qiagen) with a 15-minute on-column DNase digestion (Qiagen) to remove genomic DNA. Total RNA quality and quantity was determined with fragment analysis (University of Massachusetts Medical School Molecular Biology Core Lab) and Qubit Fluorometer (Invitrogen) analysis.
cDNA libraries were generated following a modified paired-end SMART-seq protocol (Kriegsman et al., 2019; Ramsköld et al., 2012). At least 20 ng of input RNA was used for reverse transcription with SMARTscribe reverse transcriptase (Clontech). Whole transcriptome amplification (WTA) was performed with Advantage 2 polymerase (Takara Bio). WTA reactions were monitored with qPCR to determine optimal cycle number. WTA libraries were then sized-selected with AMPure XP DNA SPRI beads (Beckman Coulter), tagmented with Tn5 transposases (Illumina Nextera XT), barcoded, and amplified with cycle number determined via qPCR monitoring. Final libraries were further size-selected with SPRI beads to an average size of 300-500 bp and quality was assessed with fragment analysis and Qubit analysis. Libraries were pooled and sequenced on a NextSeq 500 sequencer (Illumina).

treatment_protocol: Freshly harvested OT-I Rag1-/- mouse splenocytes were pooled, RBC lysed, and enriched for CD8+ cells with an EasySep negatively selective magnetic isolation kit (STEMCELL Technologies). OT-I cells were cultured at 2 x 10^5 cells per well (unless otherwise noted) and incubated with or without 50 nM (or otherwise noted) ITK/RLK inhibitor PRN-694 (Principia Biopharma) for 30 minutes 37 ̊C. Splenocytes from CD45.1+ wildtype mice were used as peptide presenting cells for easy exclusion from CD45.2+ OT-I cells via cell sorting. WT Splenocytes were cultured at 4 x 10^5 per well and incubated with indicated concentrations of OVA “N4” peptide (SIINFEKL), altered OVA “T4” peptide (SIITFEKL), or altered OVA “G4” peptide (SIITFEKL) (21st Century Biochemicals) for 60 minutes at 37 ̊C. OT-I cells and peptide loaded splenocytes were then combined and incubated at 37 ̊C for indicated stimulation times.

value: CD8+ enriched OT-I splenocytes


title: PIT_P3-PIT_P4-F1-AD010


title: CD5naiBC_D01

description: single cell RRBS


title: PIT_P1-PIT_P2-C3-AD004


title: PIT_P1-PIT_P2-A8-AD012


title: CD5naiBC_C06

description: single cell RRBS


title: PIT_P7-PIT_P8-E9-AD007


title: PIT_P3-PIT_P4-B1-AD010


title: CD5naiBC_C05

description: single cell RRBS


title: PIT_P1-PIT_P2-B5-AD008


title: PIT_P7-PIT_P8-H8-AD008


title: PIT_P5-PIT_P6-A7-AD002


title: OT-I RNA-seq 60 min. T4 peptide rep3


title: CD5naiBC_C04

description: single cell RRBS


title: PIT_P1-PIT_P2-C9-AD008


title: OT-I RNA-seq 60 min. N4 peptide rep3


title: PIT_P3-PIT_P4-A2-AD007


title: PIT_P1-PIT_P2-H11-AD010


title: PIT_P3-PIT_P4-G4-AD004


title: CD5naiBC_C03

description: single cell RRBS


title: PIT_P7-PIT_P8-A11-AD010


title: OT-I RNA-seq 60 min. N4 peptide PRN-694 rep3


title: PIT_P7-PIT_P8-E11-AD007


title: ES cells 1


title: CD5naiBC_C02

description: single cell RRBS


title: PIT_P1-PIT_P2-D5-AD006


title: PIT_P7-PIT_P8-E7-AD008


title: OT-I RNA-seq 30 min. unstimulated rep3


title: OT-I RNA-seq 30 min. T4 peptide rep3


title: OT-I RNA-seq 60 min. T4 peptide PRN-694 rep3


title: OT-I RNA-seq 30 min. T4 peptide PRN-694 rep3


title: CD5naiBC_B06

description: single cell RRBS


title: PIT_P5-PIT_P6-C2-AD002


title: PIT_P5-PIT_P6-F8-AD007


title: PIT_P7-PIT_P8-G3-AD002


title: CD5naiBC_B05

description: single cell RRBS


title: CD5naiBC_C01

description: single cell RRBS


title: OT-I RNA-seq 30 min. N4 peptide rep3


title: PIT_P3-PIT_P4-F3-AD012


title: CD5naiBC_B03

description: single cell RRBS


title: PIT_P7-PIT_P8-D2-AD002


title: PIT_P3-PIT_P4-H1-AD004


title: PIT_P7-PIT_P8-C12-AD010


title: PIT_P7-PIT_P8-D4-AD007


title: CD5naiBC_B02

description: single cell RRBS


title: PIT_P3-PIT_P4-C5-AD001


title: OT-I RNA-seq 120 min. unstimulated rep3


title: PIT_P7-PIT_P8-H2-AD012


title: PIT_P7-PIT_P8-E9-AD006


title: OT-I RNA-seq 30 min. N4 peptide PRN-694 rep3


title: PIT_P1-PIT_P2-C4-AD008


title: PIT_P5-PIT_P6-B3-AD012


title: OT-I RNA-seq 120 min. T4 peptide PRN-694 rep3


title: CD5naiBC_B01

description: single cell RRBS


title: CD5naiBC_A06

description: single cell RRBS


title: CD5naiBC_A05

description: single cell RRBS


title: OT-I RNA-seq 120 min. T4 peptide rep3


title: PIT_P5-PIT_P6-E4-AD002


title: CD5naiBC_A04

description: single cell RRBS


title: OT-I RNA-seq 120 min. N4 peptide rep3


title: OT-I RNA-seq 120 min. N4 peptide PRN-694 rep3


title: PIT_P1-PIT_P2-H2-AD010


title: PIT_P7-PIT_P8-B12-AD007


title: PIT_P5-PIT_P6-H8-AD007


title: OT-I RNA-seq 0 min. unstimulated rep3


title: PIT_P3-PIT_P4-A6-AD012


title: CD5naiBC_A02

description: single cell RRBS


title: PIT_P5-PIT_P6-E3-AD004


title: PIT_P1-PIT_P2-F1-AD006


title: PIT_P5-PIT_P6-E6-AD010


title: CD5naiBC_A01

description: single cell RRBS


title: OT-I RNA-seq 60 min. unstimulated rep2


title: PIT_P3-PIT_P4-G1-AD008


title: memBC_H12

description: single cell RRBS

value: memory B cell


title: PIT_P1-PIT_P2-C9-AD007


title: OT-I RNA-seq 60 min. T4 peptide rep2


title: PIT_P1-PIT_P2-D8-AD004


title: memBC_H11

description: single cell RRBS


title: PIT_P3-PIT_P4-D8-AD006


title: PIT_P1-PIT_P2-A6-AD002


title: PIT_P1-PIT_P2-A2-AD004


title: PIT_P5-PIT_P6-H11-AD006


title: OT-I RNA-seq 60 min. N4 peptide rep2


title: OT-I RNA-seq 60 min. T4 peptide PRN-694 rep2


title: memBC_H10

description: single cell RRBS


title: OT-I RNA-seq 60 min. N4 peptide PRN-694 rep2


title: CD5naiBC_A03

description: single cell RRBS


title: memBC_H09

description: single cell RRBS


title: PIT_P1-PIT_P2-B2-AD010


title: PIT_P3-PIT_P4-E3-AD010


title: PIT_P5-PIT_P6-E8-AD001


title: OT-I RNA-seq 30 min. unstimulated rep2


title: PIT_P1-PIT_P2-E11-AD006


title: OT-I RNA-seq 30 min. T4 peptide rep2


title: memBC_H07

description: single cell RRBS


title: PIT_P3-PIT_P4-C1-AD004


title: PIT_P5-PIT_P6-H5-AD008


title: OT-I RNA-seq 30 min. T4 peptide PRN-694 rep2


title: memBC_H08

description: single cell RRBS


title: PIT_P7-PIT_P8-F11-AD010


title: PIT_P1-PIT_P2-H3-AD010


title: PIT_P3-PIT_P4-H4-AD006


title: memBC_G11

description: single cell RRBS


title: OT-I RNA-seq 30 min. N4 peptide rep2


title: PIT_P7-PIT_P8-D1-AD001


title: PIT_P5-PIT_P6-C11-AD001


title: OT-I RNA-seq 120 min. unstimulated rep2


title: PIT_P1-PIT_P2-H1-AD002


title: OT-I RNA-seq 30 min. N4 peptide PRN-694 rep2


title: PIT_P3-PIT_P4-G7-AD007


title: PIT_P7-PIT_P8-E3-AD001


title: OT-I RNA-seq 120 min. T4 peptide rep2


title: memBC_G08

description: single cell RRBS


title: PIT_P7-PIT_P8-D8-AD002


title: PIT_P1-PIT_P2-A3-AD010


title: PIT_P1-PIT_P2-E12-AD004


title: OT-I RNA-seq 120 min. T4 peptide PRN-694 rep2


title: memBC_G07

description: single cell RRBS


title: OT-I RNA-seq 120 min. N4 peptide rep2


title: PIT_P7-PIT_P8-G3-AD007


title: PIT_P1-PIT_P2-E2-AD007


title: memBC_G12

description: single cell RRBS


title: OT-I RNA-seq 120 min. N4 peptide PRN-694 rep2


title: PIT_P1-PIT_P2-F12-AD012


title: memBC_F11

description: single cell RRBS


title: memBC_F12

description: single cell RRBS


title: PIT_P5-PIT_P6-E4-AD007


title: PIT_P7-PIT_P8-H6-AD006


title: memBC_G09

description: single cell RRBS


title: OT-I RNA-seq 0 min. unstimulated rep2


title: OT-I RNA-seq 60 min. unstimulated rep1


title: memBC_F09

description: single cell RRBS


title: memBC_G10

description: single cell RRBS


title: OT-I RNA-seq 60 min. T4 peptide rep1


title: PIT_P7-PIT_P8-H3-AD010


title: PIT_P3-PIT_P4-A11-AD006


title: PIT_P5-PIT_P6-C6-AD008


title: memBC_F08

description: single cell RRBS


title: PIT_P7-PIT_P8-E9-AD010


title: PIT_P7-PIT_P8-A9-AD006


title: PIT_P5-PIT_P6-H6-AD012


title: PIT_P1-PIT_P2-G1-AD001


title: PIT_P5-PIT_P6-C1-AD001


title: PIT_P3-PIT_P4-H12-AD012


title: OT-I RNA-seq 60 min. T4 peptide PRN-694 rep1


title: memBC_F07

description: single cell RRBS


title: OT-I RNA-seq 60 min. N4 peptide rep1


title: PIT_P5-PIT_P6-B7-AD002


title: PIT_P5-PIT_P6-C1-AD007


title: OT-I RNA-seq 60 min. N4 peptide PRN-694 rep1


title: PIT_P3-PIT_P4-F6-AD004


title: OT-I RNA-seq 30 min. unstimulated rep1


title: memBC_F10

description: single cell RRBS


title: PIT_P5-PIT_P6-H5-AD004


title: memBC_E10

description: single cell RRBS


title: memBC_E09

description: single cell RRBS


title: PIT_P5-PIT_P6-E10-AD012


title: memBC_E08

description: single cell RRBS


title: PIT_P1-PIT_P2-G10-AD006


title: PIT_P5-PIT_P6-A1-AD010


title: PIT_P5-PIT_P6-D2-AD004


title: PIT_P7-PIT_P8-F6-AD004


title: OT-I RNA-seq 30 min. N4 peptide PRN-694 rep1


title: OT-I RNA-seq 30 min. T4 peptide PRN-694 rep1


title: PIT_P7-PIT_P8-A12-AD006


title: PIT_P5-PIT_P6-E1-AD007


title: PIT_P3-PIT_P4-B11-AD004


title: PIT_P7-PIT_P8-F2-AD001


title: OT-I RNA-seq 30 min. N4 peptide rep1


title: memBC_E07

description: single cell RRBS


title: OT-I RNA-seq 30 min. T4 peptide rep1


title: PIT_P5-PIT_P6-H1-AD008


title: OT-I RNA-seq 120 min. unstimulated rep1


title: memBC_D12

description: single cell RRBS


title: OT-I RNA-seq 120 min. T4 peptide rep1


title: PIT_P5-PIT_P6-H9-AD007


title: PIT_P7-PIT_P8-D6-AD001


title: memBC_D11

description: single cell RRBS


title: memBC_D10

description: single cell RRBS


title: PIT_P5-PIT_P6-C2-AD008


title: OT-I RNA-seq 120 min. T4 peptide PRN-694 rep1


title: memBC_E12

description: single cell RRBS


title: PIT_P3-PIT_P4-B1-AD001


title: PIT_P1-PIT_P2-G9-AD001


title: memBC_E11

description: single cell RRBS


title: OT-I RNA-seq 120 min. N4 peptide rep1


title: PIT_P1-PIT_P2-E1-AD007


title: memBC_D07

description: single cell RRBS


title: memBC_D09

description: single cell RRBS


title: PIT_P1-PIT_P2-C5-AD008


title: OT-I RNA-seq 0 min. unstimulated rep1


title: PIT_P7-PIT_P8-D5-AD002


title: memBC_C11

description: single cell RRBS


title: OT-I ATAC-seq 60 min. unstimulated rep2

data_processing:
Adapter sequences were trimmed from raw sequencing reads with Cutadapt v1.3 (Martin, 2011) and were aligned to the mouse genome (mm10) with Bowtie2 v2.1.0 with the parameter -X 2000.
PCR duplicates were removed with Picard’s markDuplicates v2.17.8 and aligned reads were sorted and filtered with SAMtools v1.4.1 (Li et al., 2009).
Aligned ATAC-seq reads were trimmed to 29 bases closest to the Tn5 cut site with bedtools v2.26.0 (Quinlan and Hall, 2010) and then peaks were called with MACS2 v2.1.1 (Zhang et al., 2008) using parameters --bw 29 --nomodel -q 0.0001. Summits of called peaks across all samples were merged and “slopped” ±100bp to create a master peak reference file using bedtools v2.26.0.
Peaks were annotated with names of closest genes using a mouse OT-I TSS BED file and bedtools v2.26.0 (closest -D ref -t all). Peaks with summits within 500 bp from TSSs were labeled “promoter” peaks and summits further than 500bp were labeled “enhancer” peaks. Peak coverage for each ATAC-seq sample was calculated using bedtools v2.26.0 (intersect; coverage).
Genome_build: mm10
Supplementary_files_format_and_content: Calculated ATAC-seq peak coverage for two replicates are provided as one TSV file. Also, the same data are grouped into a DESeq2 dataset for differential expression analysis with DESeq2 v1.26.0 (Love et al., 2014). A BED file containing all peaks is also provided.

extract_protocol:
Samples of stimulated CD45.2+ OT-I cells and CD45.1+ wildtype splenocytes mixtures were stained with CD8a and CD45.2 antibodies and 7-AAD and OT-I cells were sorted (BD FACSAria) into 100% FBS and pelleted.
Precisely 50,000 stimulated OT-I T cells were FACS sorted at the same time as RNA-seq samples and pelleted in 100% FBS. ATAC-seq libraries were generated similarly as described in Buenrostro et al., 2013. Cell nuclei were isolated and transposed with 8 μL Tn5 (Illumina Nextera) at 37 ̊C for 60 minutes. DNA fragments were isolated with a Clean and Concentrator Kit (Zymo) and then Illumina barcoded and amplified with NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs). A portion of the reaction was performed as a separate qPCR reaction to determine ideal cycle number. Samples were then size selected with SPRI beads to include fragments up to 450 bp, ensuring to maintain small (<200 bp), nucleosome-free fragments. Quality of final ATAC-seq libraries was assessed with fragment analysis and Qubit analysis.


title: memBC_C12

description: single cell RRBS


title: OT-I ATAC-seq 60 min. T4 peptide rep2


title: PIT_P7-PIT_P8-C6-AD010


title: PIT_P7-PIT_P8-D7-AD010


title: OT-I ATAC-seq 60 min. N4 peptide PRN-694 rep2


title: OT-I ATAC-seq 60 min. T4 peptide PRN-694 rep2


title: PIT_P1-PIT_P2-E9-AD007


title: PIT_P1-PIT_P2-E4-AD007


title: PIT_P1-PIT_P2-H6-AD002


title: PIT_P7-PIT_P8-B10-AD008


title: memBC_C10

description: single cell RRBS


title: S_Al_long rep 3

city: Bialystok

first: Karolina

last: Chwialkowska

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

data_processing:
Sequencing data were processed to obtain fastq files with bcl2fastq2 Conversion Software v2.19.0 (Illumina, San Diego, USA) including demultiplexing and adapter trimming steps.
The quality of the obtained sequencing data was assessed before the analysis and after each of its stages, using the FastQC tool (The Babraham Institue, Cambridge, United Kingdom) and MultiQC (Ewels et al., 2016) tools. All reads were trimmed to the length of 75 bp with BBduk (DOE Joint Genomes Institute, Walnut Creek, Ca, USA). Due to the high quality of the reads, they were only soft filtered and trimmed using Sickle tool (https://github.com/najoshi/sickle). The remaining ribosomal RNA reads were then removed using the SortMeRNA software.
Clean reads were mapped to the second version of the reference genome sequence assembly of barley cv. ‘Morex’ (Morex V2; Leibniz Institute of Plant Genetics and Crop Plant Researck – IPK; Monat et al. 2019) with the splice-aware aligner STAR (Dobin et al., 2012) using two pass mode and parameters adjusted to the Morex V2 genome annotation regarding mates gaps and intron lengths.
The quality of mapping was assessed with QualiMap (Okonechnikov et al., 2016) as well as SAMStat (Lassmann et al., 2011). We applied the high confidence (HC) set of gene annotations in the Morex V2 assembly and counted reads mapping to genes using quantMode in STAR.
The analysis of differences in gene expression levels between samples was performed with the DESeq2 tool (Love et al., 2014) assuming negative binomial distribution and applying general linearized model with beta prior shrinkage.
Genome_build: Morex V2 from Leibniz Institute of Plant Genetics and Crop Plant Researck – IPK; Monat et al. 2019
Supplementary_files_format_and_content: Raw feature counts with relation to genes: gene symbols are in rows, samples in columns.

organism: Hordeum vulgare

source_name: root meristem

growth_protocol: The seeds of barley cv. ‘Sebastian’ were surface-sterilized in 5% sodium hypochlorite and incubated in dark at 4˚C for stratification. Then the seeds on Petri dishes filled with moist filter paper were put in the growth chamber at 25˚C in dark. After 48 h, the germinated seeds were transferred to 4.5 L hydroponic containers with Magnavaca solution (Magnavaca et al., 1987) for short-term and long-term experiments.

extract_protocol:
Root meristematic tissue was collected in RNAlater (Invitrogen). mRNA was isolated from root tips with the use of Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific).
The RNA-seq libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer’s instructions. Indexed libraries were pooled, clustered with use the cBot and sequenced on the Illumina HiSeq 4000 platform.

treatment_protocol: SHORT-TERM EXPERIMENT: Germinated seeds were then transferred to 4.5 L hydroponic containers with Magnavaca medium at pH=6.0 (3 containers) and pH=4.0 without aluminum (6 containers). After 48 hours of seedlings growth, the root meristems (of approximately 1-2 mm length) were collected from three containers with solution at pH=6.0 and three containers with solution at pH=4.0. Aluminum (10 µM of bioavailable Al3+ ions) was added to the remaining three containers with Magnavaca solution at pH=4.0. After 24 hours of Al treatment the root meristems were collected, as Al-treated samples. LONG-TERM EXPERIMENT: Germinated seeds were transferred to 4.5 L hydroponic containers with Magnavaca solution adjusted to pH=6.0 (3 containers) and pH=4.0 without aluminum (6 containers). After 48 hours, 10 µM of bioavailable Al3+ ions were added to three containers at pH=4.0. After further 7 days of seedlings growth, the root meristematic tissue was collected as pH=6.0, pH=4.0 and Al-treated samples.

value: root meristem

tag: cultivar

value: Sebastian

tag: conditions

value: Aluminum treatment at low pH (4.0)

tag: experiment

value: long experiment (hydroponics, 2d at pH=4 + 7d Al treatment at pH=4))


title: memBC_C09

description: single cell RRBS


title: PIT_P5-PIT_P6-F3-AD010


title: memBC_C08

description: single cell RRBS


title: memBC_C07

description: single cell RRBS


title: PIT_P1-PIT_P2-E4-AD001


title: OT-I ATAC-seq 30 min. unstimulated rep2


title: memBC_B12

description: single cell RRBS


title: PIT_P7-PIT_P8-H9-AD006


title: PIT_P7-PIT_P8-G5-AD010


title: S_Al_long rep 1


title: memBC_B10

description: single cell RRBS


title: S_pH4_long rep 3

value: low pH (4.0)

value: long experiment (hydroponics, 9d at pH=4)


title: OT-I ATAC-seq 30 min. T4 peptide PRN-694 rep2


title: memBC_B09

description: single cell RRBS


title: S_pH4_long rep 2


title: PIT_P1-PIT_P2-G2-AD001


title: PIT_P1-PIT_P2-F8-AD012


title: S_pH4_long rep 1


title: S_Al_long rep 2


title: PIT_P1-PIT_P2-H9-AD002


title: memBC_A12

description: single cell RRBS


title: memBC_A11

description: single cell RRBS


title: PIT_P3-PIT_P4-E5-AD007


title: PIT_P3-PIT_P4-G4-AD006


title: OT-I ATAC-seq 60 min. N4 peptide rep2


title: OT-I ATAC-seq 30 min. T4 peptide rep2


title: S_pH6_long rep 2

value: optimal pH (6.0)

value: long experiment (hydroponics, 9d at pH=6)


title: memBC_A10

description: single cell RRBS


title: OT-I ATAC-seq 120 min. unstimulated rep2


title: PIT_P1-PIT_P2-B1-AD002

value: Pituitary

value: male


title: OT-I ATAC-seq 120 min. T4 peptide rep2


title: S_pH6_long rep 1


title: PIT_P5-PIT_P6-F6-AD010


title: memBC_A09

description: single cell RRBS

value: HD


title: OT-I ATAC-seq 120 min. T4 peptide PRN-694 rep2


title: memBC_A08

description: single cell RRBS


title: memBC_A07

description: single cell RRBS


title: OT-I ATAC-seq 30 min. N4 peptide rep2


title: S_pH6_long rep 3


title: S_Al_short rep 2

value: short experiment (hydroponics, 48h at pH=4 + 24h Al treatment at pH=4)


title: OT-I ATAC-seq 120 min. N4 peptide rep2


title: PIT_P3-PIT_P4-C11-AD001


title: S_Al_short rep 1


title: PIT_P5-PIT_P6-A11-AD006


title: naiBC_H04

description: single cell RRBS

value: naive B cell


title: OT-I ATAC-seq 0 min. unstimulated rep2


title: S_pH6_short rep 3

value: short experiment (hydroponics, 48h at pH=4)


title: PIT_P7-PIT_P8-B10-AD001


title: OT-I ATAC-seq 60 min. unstimulated rep1


title: S_pH6_short rep 2


title: naiBC_G06

description: single cell RRBS


title: PIT_P1-PIT_P2-C3-AD010


title: PIT_P7-PIT_P8-G12-AD002


title: OT-I ATAC-seq 60 min. T4 peptide rep1


title: naiBC_G05

description: single cell RRBS


title: OT-I ATAC-seq 60 min. T4 peptide PRN-694 rep1


title: PIT_P1-PIT_P2-E6-AD008


title: S_Al_short rep 3


title: S_pH4_short rep 3

value: short experiment (hydroponics, 48h at pH=6)


title: PIT_P5-PIT_P6-H6-AD007


title: naiBC_G04

description: single cell RRBS


title: OT-I ATAC-seq 120 min. N4 peptide PRN-694 rep2

value: CD8+ enriched OT-I splenocytes


title: S_pH4_short rep 2


title: OT-I ATAC-seq 60 min. N4 peptide rep1


title: naiBC_G02

description: single cell RRBS


title: naiBC_H02

description: single cell RRBS


title: PIT_P5-PIT_P6-A11-AD007


title: naiBC_G03

description: single cell RRBS


title: PIT_P1-PIT_P2-A9-AD010


title: S_pH4_short rep 1


title: OT-I ATAC-seq 30 min. unstimulated rep1


title: OT-I ATAC-seq 30 min. T4 peptide rep1


title: naiBC_F06

description: single cell RRBS


title: PIT_P3-PIT_P4-G12-AD012


title: naiBC_G01

description: single cell RRBS


title: Microwell Round_Day40_Rep1

city: Raleigh

first: Albert

middle: J

last: Keung

address: 911 Partners Way

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

data_processing:
Raw FASTQ formatted sequence reads were imported into CLC Genomics Workbench (version 20.0.2, QIAGEN Digital Insights)
Adaptor sequences and bases with low quality were trimmed and reads were mapped to the reference genome (GRCh38.102) using the RNAseq analysis tool with the default parameters recommended for RNAseq analysis in CLC Genomics Workbench (version 20.0.2, QIAGEN Digital Insights).
Gene expression is estimated with the EM estimation algorithm and reported as TPM (Transcripts Per Million)  and RPKM (Reads per kilobase of transcript per million mapped reads) using CLC Genomics Workbench (version 20.0.2, QIAGEN Digital Insights).
Genome_build: GRCh38.102
Supplementary_files_format_and_content: All process data files are .xlsx files including name, chromosome, region, expression value, TPM, RPKM, exons, gene ID, gene length, ENSEMBL ID, biotype, unique reads, total reads, annotated transcripts, uniquely identified transcripts, exon length, unique exon reads, total exon reads, ratio of unique to total exon reads, unique exon-exon reads, total exon-exon reads, unique intron reads, total intron reads and ratio of intron to total gene reads for each gene.

source_name: Human cerebral organoids

growth_protocol: Feeder-independent H9 human embryonic stem cells (hESCs) (WA09) were obtained from WiCell. Cells were maintained in tissue culture dishes (Fisher Scientific Corning Costar) coated with 0.5 mg/cm2 Vitronectin (VTN-N) (Thermo Fisher Scientific) in E8 medium (Thermo Fisher Scientific) and passaged using standard protocols. 96-well and microwell human cerebral organoids (hCOs) were generated using the same pool of hESCs and differentiated using the same protocol as previously described (Lancaster et al. 2013, Nature). Number of cells seeded per well was experimentally optimized for successful generation of embryos bodies (EB) in microwells. For each microwell device, 60 µL of hESC suspension at 32,000 cells/well was pipetted into the microwell enclosure using a cut p200 tip. The device was gently placed into the incubator for 5 minutes to allow cells to settle into the microwells. After 5 minutes, 2.5 mL media was slowly added to the wells avoiding the disruption of the seeded cells in the microwells. Media was changed every 12 hours for the first 3 days with fresh hESC medium with basic fibroblast growth factor (bFGF) (Invitrogen) and ROCK inhibitor (Y-27632, LC laboratories) for all hCOs (microwell and 96-well). All cells and hCOs were maintained in a humid incubator at 37 °C with 5 % CO2. After 5 days all hCOs were transferred into low-attachment 24-wells plates (1 hCO/well) and the remainder of the previously described whole brain organoid protocol was followed (Lancaster et al. 2013, Nature).

extract_protocol:
For total RNA extraction the following samples were collected from three independent culture plates: 10 pooled human cerebral organids (hCO) for day 10 samples, 6 pooled hCOs for day 20 samples, and 4 pooled hCOs for day 40 samples. hCOs were washed 3 times in cold PBS. Matrigel was dissolved by incubating the hCOs in chilled Cell Recovery Solution (Corning, cat. no. 354253) for 1h at 4 °C. The dissolved Matrigel was removed by rinsing 3 times in cold PBS. Total RNA was isolated using Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s protocol. RNA samples were collected in 2mL RNAse-free tubes and chilled on ice throughout the procedure.
RNA libraries were prepared and sequenced by BGI using DNB-seq PE100 platform.

tag: cell line

value: H9 human embryonic stem cells (WA09, WiCell)

tag: time point

value: Day 40

tag: embryoid body formation method

value: Agarose microwell shape round


title: Microwell Round_Day40_Rep2


title: Microwell Round_Day40_Rep3


title: S_pH6_short rep 1

value: root meristem

value: Sebastian


title: naiBC_F05

description: single cell RRBS


title: Microwell Butterfly_Day40_Rep3

value: Agarose microwell shape butterfly


title: naiBC_F04

description: single cell RRBS


title: OT-I ATAC-seq 30 min. N4 peptide rep1

tag: cell type


title: PIT_P5-PIT_P6-H10-AD007


title: OT-I ATAC-seq 60 min. N4 peptide PRN-694 rep1


title: naiBC_F03

description: single cell RRBS


title: PIT_P3-PIT_P4-G2-AD004


title: naiBC_F02

description: single cell RRBS


title: OT-I ATAC-seq 120 min. unstimulated rep1


title: PIT_P7-PIT_P8-C1-AD004


title: PIT_P7-PIT_P8-A2-AD006


title: Microwell Butterfly_Day40_Rep1


title: OT-I ATAC-seq 30 min. N4 peptide PRN-694 rep1


title: naiBC_F01

description: single cell RRBS


title: PIT_P5-PIT_P6-D12-AD001


title: OT-I ATAC-seq 30 min. T4 peptide PRN-694 rep1


title: Microwell Butterfly_Day40_Rep2


title: PIT_P3-PIT_P4-E7-AD007


title: OT-I ATAC-seq 120 min. T4 peptide PRN-694 rep1


title: naiBC_E04

description: single cell RRBS


title: Microwell Peanut_Day40_Rep2

value: Agarose microwell shape peanut


title: naiBC_E03

description: single cell RRBS


title: OT-I ATAC-seq 120 min. T4 peptide rep1


title: OT-I ATAC-seq 120 min. N4 peptide rep1


title: OT-I ATAC-seq 120 min. N4 peptide PRN-694 rep1


title: PIT_P5-PIT_P6-C10-AD010


title: PIT_P5-PIT_P6-C7-AD004


title: naiBC_E02

description: single cell RRBS


title: Microwell C_Day40_Rep3

value: Agarose microwell shape C


title: PIT_P5-PIT_P6-D1-AD004


title: OT-I ATAC-seq 0 min. unstimulated rep1


title: Microwell C_Day40_Rep2


title: naiBC_E01

description: single cell RRBS


title: Microwell Peanut_Day40_Rep3


title: PIT_P1-PIT_P2-F1-AD007


title: PIT_P1-PIT_P2-F2-AD004


title: Microwell C_Day40_Rep1


title: 96-well_Day40_Rep3

value: Low attachment U-bottom 96-well plate


title: naiBC_D06

description: single cell RRBS


title: WT_HDF_3_Hi_S6

city: Jinju

first: Gu

middle: Seob

last: Roh

address: Jinju, Gyeongnam, Republic of Korea

department: Department of Anatomy and Convergence Medical Science, College of Medicine

country: South Korea

institute: Gyeongsang National University

data_processing:
RawdataQC checking with Trimmomatic v0.36   with PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:10
Read Alignment by Hisat2-2.0.5 with default parameter
Read count by FeatureCount 1.5.0-p2 with default parameter
Genome_build: GRCm38
Supplementary_files_format_and_content: Ob_Mus_RNA_seq_counts.txt

extract_protocol:
Total mRNA from hearts was isolated using TRIzol and reverse-transcribed using the RevertAid First-Strand cDNA Synthesis Kit. The sequencing library was constructed using Illumina’s TruSeq RNA Prep kit, and data generation was performed following the manufacturer’s protocol with NextSeq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

tag: diet

value: HFD

value: Hi


title: ob_ob_ND_2_Hy_S20

value: ND

tag: tissue

value: Hy


title: WT_ND_1_Hi_S1


title: 96-well_Day40_Rep1


title: PIT_P7-PIT_P8-E4-AD006

value: Pituitary

tag: age

value: male


title: Microwell Peanut_Day40_Rep1


title: PIT_P5-PIT_P6-B12-AD010

tag: strain


title: Microwell Round_Day20_Rep3

value: Day 20


title: naiBC_D02

description: single cell RRBS

value: HD

value: naive B cell


title: PIT_P7-PIT_P8-D3-AD007

tag: Sex


title: PIT_P1-PIT_P2-A11-AD007


title: ob_ob_ND_2_Li_S8

value: Li


title: WT_HFD_1_Li_S4


title: naiBC_D01

description: single cell RRBS

tag: patient id


title: PIT_P7-PIT_P8-A2-AD001


title: naiBC_C06

description: single cell RRBS

tag: diagnosis


title: Microwell Round_Day20_Rep2

value: H9 human embryonic stem cells (WA09, WiCell)

value: Agarose microwell shape round


title: WT_ND_3_Ep_S15

value: Ep


title: naiBC_D03

description: single cell RRBS

tag: ighv


title: ob_ob_HFD_1_Ao_S22

value: Ao


title: PIT_P5-PIT_P6-B10-AD004


title: Microwell Butterfly_Day20_Rep3

value: Agarose microwell shape butterfly


title: naiBC_D04

description: single cell RRBS

tag: treatmentstatus


title: naiBC_C05

description: single cell RRBS


title: PIT_P3-PIT_P4-C8-AD008


title: 96-well_Day40_Rep2

value: Day 40

value: Low attachment U-bottom 96-well plate


title: ob_ob_HFD_1_Ep_S22

tag: genotype

value: HFD


title: naiBC_C03

description: single cell RRBS


title: Microwell Round_Day20_Rep1


title: Microwell Butterfly_Day20_Rep2


title: PIT_P7-PIT_P8-A10-AD010


title: ob_ob_ND_2_He_S8

value: He


title: ob_ob_HFD_2_Sk_S11

value: Sk


title: Microwell Butterfly_Day20_Rep1


title: naiBC_B04

description: single cell RRBS


title: PIT_P7-PIT_P8-D4-AD010


title: naiBC_C01

description: single cell RRBS


title: naiBC_C02

description: single cell RRBS


title: ob_ob_HFD_3_Ao_S24


title: Microwell Peanut_Day20_Rep3

value: Agarose microwell shape peanut


title: ob_ob_HFD_1_Hy_S22

value: Hy


title: PIT_P3-PIT_P4-G8-AD007

value: Pituitary

value: male


title: Microwell Peanut_Day20_Rep2

value: Day 20


title: naiBC_A06

description: single cell RRBS

value: HD

value: naive B cell


title: PIT_P1-PIT_P2-B11-AD010


title: ob_ob_HFD_1_Li_S10

value: Li


title: naiBC_A02

description: single cell RRBS


title: ob_ob_ND_3_Sk_S9

value: ND


title: naiBC_A01

description: single cell RRBS


title: Microwell Peanut_Day20_Rep1

value: H9 human embryonic stem cells (WA09, WiCell)


title: Microwell C_Day20_Rep3

value: Agarose microwell shape C


title: PIT_P1-PIT_P2-H1-AD001


title: MBL_sc08_D12

description: single cell RRBS

value: MBL 08

value: MBL

value: pre-treatment


title: WT_ND_1_Sk_S1

value: WT


title: WT_ND_3_Ao_S15

value: Ao


title: PIT_P7-PIT_P8-B10-AD007


title: MBL_sc08_D10

description: single cell RRBS


title: Microwell C_Day20_Rep2


title: PIT_P7-PIT_P8-B9-AD012


title: MBL_sc08_D09

description: single cell RRBS


title: 96-well_Day20_Rep3

value: Low attachment U-bottom 96-well plate


title: OT-I ATAC-seq 30 min. N4 peptide PRN-694 rep2

value: CD8+ enriched OT-I splenocytes


title: PIT_P3-PIT_P4-B12-AD002


title: WT_HDF_3_Hy_S18

value: HFD

value: Hy


title: MBL_sc08_D08

description: single cell RRBS


title: Microwell C_Day20_Rep1


title: PIT_P1-PIT_P2-H7-AD010

value: Pituitary

value: male


title: 96-well_Day20_Rep2

value: Day 20


title: 96-well_Day20_Rep1


title: PIT_P3-PIT_P4-F7-AD008


title: MBL_sc08_D07

description: single cell RRBS


title: WT_ND_2_Hi_S2

value: Hi


title: PIT_P5-PIT_P6-E7-AD004


title: ob_ob_HFD_3_Li_S12

value: Li


title: Microwell Butterfly_Day10_Rep3

value: Day 10

value: Agarose microwell shape butterfly


title: MBL_sc08_D05

description: single cell RRBS


title: Microwell Butterfly_Day10_Rep2

value: H9 human embryonic stem cells (WA09, WiCell)


title: PIT_P5-PIT_P6-A3-AD004


title: MBL_sc08_D04

description: single cell RRBS

value: MBL 08


title: ob_ob_ND_3_Ep_S21

value: ND

value: Ep


title: PIT_P7-PIT_P8-E12-AD012


title: WT_ND_3_He_S3

value: WT

value: He


title: WT_HFD_3_Ep_S18


title: MBL_sc08_D03

description: single cell RRBS

value: MBL

value: pre-treatment


title: Microwell Butterfly_Day10_Rep1


title: Microwell Round_Day10_Rep3

value: Agarose microwell shape round


title: PIT_P3-PIT_P4-H6-AD006


title: WT_ND_2_Sk_S2

value: Sk


title: PIT_P3-PIT_P4-B10-AD008

value: Pituitary


title: ob_ob_ND_2_Sk_S8


title: MBL_sc08_D01

description: single cell RRBS


title: PIT_P3-PIT_P4-C5-AD008

value: male


title: MBL_sc08_C12

description: single cell RRBS


title: WT_HFD_2_He_S5

value: HFD


title: Microwell Round_Day10_Rep1


title: PIT_P1-PIT_P2-B2-AD001


title: Microwell Peanut_Day10_Rep3

value: Agarose microwell shape peanut


title: MBL_sc08_C09

description: single cell RRBS


title: PIT_P3-PIT_P4-C2-AD008


title: MBL_sc08_C08

description: single cell RRBS


title: MBL_sc08_C10

description: single cell RRBS


title: Microwell Peanut_Day10_Rep2


title: PIT_P5-PIT_P6-E1-AD006


title: WT_ND_2_Ao_S14

value: Ao


title: Microwell Peanut_Day10_Rep1

value: Day 10


title: ob_ob_ND_3_He_S9


title: PIT_P5-PIT_P6-E11-AD007


title: MBL_sc08_C06

description: single cell RRBS


title: Microwell C_Day10_Rep3

value: Agarose microwell shape C


title: PIT_P7-PIT_P8-A10-AD006


title: ob_ob_ND_2_Ao_S20


title: Microwell C_Day10_Rep2

value: H9 human embryonic stem cells (WA09, WiCell)


title: MBL_sc08_C05

description: single cell RRBS

value: MBL 08


title: Microwell Round_Day10_Rep2


title: Microwell C_Day10_Rep1


title: WT_HFD_3_He_S6


title: PIT_P3-PIT_P4-A8-AD002


title: WT_ND_3_Li_S3

value: ND

value: Li


title: PIT_P3-PIT_P4-D8-AD012


title: MBL_sc08_C03

description: single cell RRBS


title: WT_ND_1_Ao_S13

value: WT


title: WT_HFD_2_Li_S5


title: PIT_P5-PIT_P6-H5-AD012


title: MBL_sc08_C01

description: single cell RRBS


title: ob_ob_ND_1_Ep_S19

value: Ep


title: 96-well_Day10_Rep3

value: Low attachment U-bottom 96-well plate


title: MBL_sc08_B12

description: single cell RRBS

value: MBL

value: pre-treatment


title: PIT_P5-PIT_P6-D5-AD006


title: MBL_sc08_C07

description: single cell RRBS


title: 96-well_Day10_Rep1


title: MBL_sc08_B11

description: single cell RRBS


title: WT_HFD_1_Sk_S4

value: Sk


title: PIT_P3-PIT_P4-E3-AD002

value: Pituitary


title: ob_ob_HFD_2_Li_S11


title: MBL_sc08_B10

description: single cell RRBS


title: PIT_P7-PIT_P8-B8-AD004

value: male


title: MBL_sc08_B09

description: single cell RRBS


title: PIT_P7-PIT_P8-A11-AD004


title: ob_ob_ND_2_Ep_S20


title: ob_ob_HFD_3_Ep_S24

value: HFD


title: WT_ND_1_Hy_S13

value: Hy


title: PIT_P3-PIT_P4-A8-AD008


title: PIT_P5-PIT_P6-B9-AD012


title: 96-well_Day10_Rep2


title: MBL_sc08_B07

description: single cell RRBS


title: MBL_sc08_B08

description: single cell RRBS


title: Treatment group 2-rep 1-NK1.1+

type: RNA

city: Houston

first: vanaja

last: konduri

state: Texas

address: One Baylor Plaza

department: Pathology&Immunology

institute: Baylor College of Medicine

description: RMA expression value derived from Transcriptome Analysis Console v3.0

hyb_protocol: Samples were hybridized with GeneChip mouse WT Pico-Clariom D Exon Arrays (Affymetrix) and scanned at the Sequencing and Microarray Facility at the University of Texas MDAnderson Cancer Center.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with Transcriptome Analysis Console v3.0 (Affymetrix).  Data analysis and statistical evaluations were performed with R version 3.4.3. Class comparison paired T test was used with an FDR of 0.05% to 0.1%.

label: biotin

source_name: SPLENOCYTES

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated from the cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA.

treatment_protocol: CD8+CD69+NK1.1+ and CD8+CD69+NK1.1- T cells were sorted by flow cytometry from mouse splenocytes antigenically stimulated overnight.

tag: cells

value: CD8+CD69+NK1.1+ T cells

tag: treatment

value: Drug Alone


title: Treatment group 2-rep 2-Nk1.1+


title: Treatment group 1-rep 3-Nk1.1-

value: CD8+CD69+NK1.1- T cells

value: Double Loaded DC + Drug


title: MBL_sc08_B06

description: single cell RRBS

value: MBL 08


title: PIT_P5-PIT_P6-E12-AD002


title: MBL_sc08_B05

description: single cell RRBS


title: WT_ND_2_Ep_S14

value: ND


title: PIT_P7-PIT_P8-D4-AD008


title: MBL_sc08_B04

description: single cell RRBS


title: PIT_P3-PIT_P4-H3-AD010


title: Treatment group1-rep 2-Nk1.1+


title: Treatment group 1-rep 2-Nk1.1-


title: MBL_sc08_B02

description: single cell RRBS


title: Treatment group 1-rep 1-Nk1.1-


title: ob_ob_ND_1_Sk_S7


title: WT_ND_1_Ep_S13


title: ob_ob_ND_1_Hy_S19


title: MBL_sc08_B01

description: single cell RRBS


title: PIT_P7-PIT_P8-D6-AD008


title: ob_ob_HFD_1_He_S10

value: He


title: PIT_P7-PIT_P8-E8-AD010


title: WT_HFD_1_He_S4

value: WT


title: PIT_P3-PIT_P4-C8-AD006


title: MBL_sc08_A12

description: single cell RRBS


title: WT_ND_2_He_S2


title: PIT_P3-PIT_P4-H11-AD002


title: MBL_sc08_A11

description: single cell RRBS


title: WT_ND_3_Hy_S15


title: PIT_P3-PIT_P4-F3-AD010


title: MBL_sc08_A10

description: single cell RRBS


title: PIT_P1-PIT_P2-B3-AD007


title: ob_ob_ND_3_Ao_S21

value: Ao


title: WT_HFD_2_Sk_S5


title: PIT_P1-PIT_P2-B10-AD001


title: PIT_P3-PIT_P4-G12-AD010


title: WT_ND_1_He_S1


title: MBL_sc08_A07

description: single cell RRBS


title: MBL_sc08_A06

description: single cell RRBS


title: PIT_P3-PIT_P4-C9-AD012


title: MBL_sc08_A05

description: single cell RRBS


title: ob_ob_HFD_1_Hi_S10

value: Hi


title: WT_HDF_1_Hy_S16


title: PIT_P1-PIT_P2-A3-AD002


title: MBL_sc08_A09

description: single cell RRBS

value: MBL


title: PIT_P3-PIT_P4-B12-AD006


title: MBL_sc08_A08

description: single cell RRBS

value: pre-treatment


title: MBL_sc08_A04

description: single cell RRBS


title: murine kidney_non-pathogenic Leptospira spp.-infected_28d_ biological rep2

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

description: Expression data from infected mice kidney tissue

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with SST-RMA by Affymetrix Expression Console Ver 1.4

source_name: Kidney from mice infected with non-pathogenic Leptospira spp after 28 days

label_protocol: Standard Affymetrix protocol

growth_protocol: C57BL/6 female mice aged 6–8 weeks were used for this study. All animal experiments were handled under Animal Biosafety Level 2 conditions and followed all appropriate guidelines for the use of infected animals.

extract_protocol: Total RNA was extracted from kidney tissues using the TRIzol reagent (Invitrogen, Carlsbad, CA) with DNaseI digestion. The quantity and integrity of extracted RNA were verified using a Nano-Drop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The resulting RNA samples with RNA integrity values of > 7.0, were used for Affymetrix whole-transcriptome gene expression analysis.

treatment_protocol: Bacteria were propagated at 28 °C under aerobic conditions in medium containing 10 % Leptospira enrichment Elinghausen-McCullough-Johnson-Harris (EMJH) medium (BD Diagnostics) and 90 % Leptospira medium base EMJM medium (Difco, Sparks, MD). Bacterial densities were measured using a CASY-Model TT cell counter and analyzer (Casy-Technology, Roche Innovatis AG, Reutlingen, Germany). Mice were inoculated using intraperitoneal challenge with a high infective dose of Leptospira spp. (above 2x10^8 leptospires in 0.1 ml EMJH medium), and the control groups were inoculated with sterile EMJH medium .

value: female

tag: infected with

value: L. biflexa serovar Patoc

tag: infection duration

value: 28 days

value: kidney

tag: mouse genotype

value: wildtype

value: 6-8 weeks


title: Treatment group 1-rep 1-Nk1.1+

value: CD8+CD69+NK1.1+ T cells


title: WT_ND_3_Sk_S3

value: Sk


title: murine kidney_non-pathogenic Leptospira spp.-infected_28d_ biological rep3


title: murine kidney_non-pathogenic Leptospira spp.-infected_7d_ biological rep2

source_name: Kidney from mice infected with non-pathogenic Leptospira spp after 7 days

value: 7 days


title: murine kidney_non-pathogenic Leptospira spp.-infected_28d_ biological rep1


title: murine kidney_non-pathogenic Leptospira spp.-infected_7d_ biological rep1


title: WT_ND_2_Li_S2

value: Li


title: WT_HDF_2_Hy_S17

value: HFD

value: Hy


title: murine kidney_pathogenic Leptospira spp.-infected_28d_ biological rep3

source_name: Kidney from mice infected with pathogenic Leptospira spp after 28 days

value: L. interrogans serovar Copenhageni Fiocruz L1-130


title: PIT_P5-PIT_P6-C10-AD002

value: Pituitary

value: male


title: murine kidney_pathogenic Leptospira spp.-infected_28d_ biological rep2


title: murine kidney_non-pathogenic Leptospira spp.-infected_7d_ biological rep3


title: MBL_sc08_A03

description: single cell RRBS

value: MBL 08

value: MBL


title: murine kidney_pathogenic Leptospira spp.-infected_7d_ biological rep3

source_name: Kidney from mice infected with pathogenic Leptospira spp after 7 days

value: female


title: murine kidney_pathogenic Leptospira spp.-infected_7d_ biological rep2


title: WT_ND_2_Hy_S14

value: WT

value: ND


title: murine kidney_pathogenic Leptospira spp.-infected_7d_ biological rep1

value: kidney


title: PIT_P7-PIT_P8-A3-AD004


title: murine kidney_pathogenic Leptospira spp.-infected_28d_ biological rep1

value: 28 days

value: wildtype


title: MBL_sc08_A02

description: single cell RRBS

value: pre-treatment


title: WT_ND_3_Hi_S3

value: Hi


title: PIT_P5-PIT_P6-B2-AD010


title: MBL_sc05_H4

description: single cell RRBS

value: MBL 05


title: ob_ob_HFD_2_Ep_S23

value: Ep


title: MBL_sc05_H3

description: single cell RRBS


title: PIT_P3-PIT_P4-E8-AD012


title: ob_ob_HFD_2_Hy_S23

value: HFD


title: PIT_P3-PIT_P4-F9-AD008


title: PIT_P7-PIT_P8-G11-AD002


title: ob_ob_ND_1_Li_S7

value: Li


title: ob_ob_ND_3_Li_S9


title: PIT_P5-PIT_P6-G10-AD007


title: PIT_P1-PIT_P2-G2-AD007


title: WT_HFD_1_Ep_S16


title: WT_HFD_3_Li_S6


title: PIT_P5-PIT_P6-D11-AD006


title: ob_ob_HFD_3_Hy_S24

value: Hy


title: PIT_P5-PIT_P6-G9-AD010

value: Pituitary


title: PIT_P1-PIT_P2-B1-AD001

value: male


title: ob_ob_HFD_2_Ao_S23

value: Ao


title: MBL_sc05_H2

description: single cell RRBS

value: MBL


title: MBL_sc05_G2

description: single cell RRBS


title: MBL_sc05_H1

description: single cell RRBS


title: MBL_sc05_G4

description: single cell RRBS


title: MBL_sc05_G1

description: single cell RRBS


title: MBL_sc05_G3

description: single cell RRBS


title: S2 Fne WT

city: New York

first: Seungjae

last: Lee

state: NY

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

data_processing:
Total RNA-seq data were mapped to the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6).
For BrdU-CLIP, raw CLIP-seq reads were processed by trimming of adaptors by Cutadapt v1.18, and all reads were required to have a length of at least 29 bp containing 14 nt random barcode. The filtered reads were collapsed then random barcodes were trimmed. Remaining reads were mapped to unique positions in the Drosophila melanogaster genome (UCSC version dm6) using Burrows-Wheeler Aligner (BWA 0.7.17), allowing mismatches depending on read length with parameter -n 0.06.
Genome_build: dm6

organism: Drosophila melanogaster

growth_protocol: S2R+ cells were maintained at 25℃ in standard Schneider insect medium supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNAs were extracted from S2R+ cells transfected as described above using Trizol.
Total RNA-seq libraries of L1CNS samples were prepared using TruSeq Stranded Total RNA Library Preparation Kit (Illumina) with 2 ug total RNA as starting materials for each sample.
BrdU-CLIP libraries were made using S2R+ cells with overexpression of wildtype Elav, Rbp9, Fne and their RRM3XMT counterparts based on published with some optimizations. Protein-RNA complexes are immune-precipitated using anti-FLAG antibody (Sigma Aldrich) followed by stringent washes and ligation of the 3’ linker. After digestion of the protein, the RNA is purified and reverse transcribed using a dNTP mix where dTTP is replaced with BrdUTP. The RT primer has 5’ and 3’ anchor sequences used later for PCR amplification separated by an APE1 cleavage site. The BrdUTP incorporated into the resulting cDNA allows on-bead cDNA purification using anti-BrdU antibody (Sigma Aldrich). The purified cDNA is then circularized and re-linearized on-bead using CircLigase II and APE1, respectively, which places the two PCR anchors in the correct orientation.

treatment_protocol: S2R+ cells were transfected with wildtype Elav, Rbp9, Fne and RRM mutant versions of Elav, Rbp9, Fne using Qiangen Effectene according to manufacture' s instructions.

tag: transfection

value: WT_Fne transfected


title: S2 Elav WT CLIP

tag: cell type

value: WT_Elav transfected

tag: antibody

value: BrdU-CLIP


title: S2 Elav 3X CLIP

value: RRM_3X_Elav transfected


title: PIT_P5-PIT_P6-A2-AD004

tag: tissue


title: ob_ob_HFD_3_Sk_S12

tag: diet

value: Sk


title: S2 Fne 3X

value: RRM_3X_Fne transfected


title: S2 Rbp9 WT

value: WT_Rbp9 transfected


title: ob_ob_ND_1_Ao_S19

value: ND


title: PIT_P1-PIT_P2-F2-AD010

tag: age

tag: strain


title: S2 Rbp9 3X

value: RRM_3X_Rbp9 transfected


title: murine kidney_non-infected_28d_ biological rep2

description: Expression data from non-infected mice kidney tissue, at day 28

source_name: Kidney from mice inoculated with sterile EMJH medium after 28 days

tag: Sex

value: female

value: kidney

value: wildtype

value: 6-8 weeks


title: PIT_P1-PIT_P2-H11-AD001

value: Pituitary


title: murine kidney_non-infected_28d_ biological rep1


title: MBL_sc05_F4

description: single cell RRBS

tag: patient id

value: MBL 05

tag: diagnosis

value: pre-treatment


title: murine kidney_non-infected_28d_ biological rep3


title: S2 Elav WT


title: murine kidney_non-infected_7d_ biological rep2

description: Expression data from non-infected mice kidney tissue, at day 7

source_name: Kidney from mice inoculated with sterile EMJH medium after 7 days


title: murine kidney_non-infected_7d_ biological rep3


title: murine kidney_non-infected_7d_ biological rep1


title: WT_HFD_1_Ao_S16

value: WT

value: HFD

value: Ao


title: MBL_sc05_E4

description: single cell RRBS

value: MBL

tag: ighv

tag: treatmentstatus


title: PIT_P7-PIT_P8-C11-AD007

value: male


title: MBL_sc05_F2

description: single cell RRBS


title: MBL_sc05_F3

description: single cell RRBS


title: ob_ob_ND_1_Hi_S7

tag: genotype

value: Hi


title: WT_HFD_2_Ao_S17


title: MBL_sc05_E3

description: single cell RRBS


title: PIT_P1-PIT_P2-C5-AD002


title: ob_ob_ND_1_He_S7

value: He


title: In vitro dHF overexpressing Gb4S

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

description: genetically modified with lentiviral vector to overexpress Gb4 synthase

data_processing:
Cell Ranger 2.1.1 was used to convert Illumina base call files to FASTQ format.
Cell Ranger 3.1.0 was used to map FASTQ sequencing reads to the human GRCh38 reference transcriptome  and to generate feature-barcode count matrices.
Downstream analyses, including dimensionality reduction and cell type annotation, were performed using both velocyto and scanpy in Python (version 3.7)
Genome_build: GRCh38 human reference

source_name: prmary culture of human dermal fibroblasts (transduced)

extract_protocol:
initial lines were transduced with lentiviral vector, the selection with Blasticidin for stable transduction was performed
10x v3.1 single index protocol was used for samples 1-4, 10x v3.1 dual index protocol was used for samples 5-9
scRNA-seq (10x v3.1)

value: human skin


title: S2 Cntr

value: non transfected


title: S2 Elav 3X

value: RRM_3X_Elav transfected


title: In vitro dHF overexpressing GM3S replica 2

description: genetically modified with lentiviral vector to overexpress GM3 synthase


title: WT_HFD_3_Ao_S18


title: PIT_P3-PIT_P4-H1-AD010


title: MBL_sc05_E2

description: single cell RRBS


title: In vitro dHF empty vector transduced replica 2

description: genetically modified with lentiviral vector (empty)


title: MBL_sc05_E1

description: single cell RRBS


title: MBL_sc05_F1

description: single cell RRBS


title: ob_ob_ND_2_Hi_S8

value: ND


title: In vitro dHF overexpressing GM3S replica 1


title: PIT_P1-PIT_P2-B9-AD007


title: MBL_sc05_D4

description: single cell RRBS


title: PIT_P7-PIT_P8-C8-AD010


title: ob_ob_ND_3_Hi_S9


title: In vitro dHF empty vector transduced replica 1


title: MBL_sc05_D2

description: single cell RRBS


title: PIT_P3-PIT_P4-D6-AD008


title: ob_ob_ND_3_Hy_S21

value: Hy


title: MBL_sc05_D1

description: single cell RRBS


title: PIT_P3-PIT_P4-H2-AD004


title: MBL_sc05_C4

description: single cell RRBS


title: WT_HDF_1_Hi_S4


title: In vitro dHF replica 2

source_name: prmary culture of human dermal fibroblasts

extract_protocol:
received as a gift from Paolo Dotto Lab
10x v3.1 single index protocol was used for samples 1-4, 10x v3.1 dual index protocol was used for samples 5-9
scRNA-seq (10x v3.1)


title: In vitro dHF treated with Fumonisin B1 replica 1


title: MBL_sc05_C3

description: single cell RRBS


title: MBL_sc05_C2

description: single cell RRBS


title: WT_HFD_2_Ep_S17

value: Ep


title: WT_HDF_2_Hi_S5


title: PIT_P5-PIT_P6-C6-AD007


title: PIT_P5-PIT_P6-H8-AD004


title: PIT_P7-PIT_P8-C10-AD010


title: MBL_sc05_C1

description: single cell RRBS


title: In vitro dHF replica 1


title: PIT_P1-PIT_P2-A1-AD010


title: ob_ob_HFD_3_Hi_S12


title: MBL_sc05_B4

description: single cell RRBS


title: MBL_sc08_B03

description: single cell RRBS

value: MBL 08


title: WT_ND_1_Li_S1

value: Li


title: PIT_P5-PIT_P6-E3-AD002

value: Pituitary


title: In vitro dHF treated with Fumonisin B1 replica 2


title: ob_ob_HFD_1_Sk_S10

value: Sk


title: PIT_P1-PIT_P2-D1-AD010


title: PIT_P5-PIT_P6-H2-AD012


title: MBL_sc05_B2

description: single cell RRBS

value: MBL 05

value: pre-treatment


title: PIT_P5-PIT_P6-D2-AD012


title: WT_HFD_3_Sk_S6

value: WT

value: HFD


title: Liver-Tunil-3

city: Beijing

first: Peng

last: Ma

address: 1 Xian Nong Tan Street

department: Institute of Materia Medica

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: liver from tunicamycin-injected mice

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: After adaptive feeding, Tuni group mice were injected intraperitoneally with 2.5mg/kg tunicamycin (T101151, Aladdin, Shanghai, China) while Ctrl (control) group were injected the same volume vehicle. PBS (G4202, Servicebio, Wuhan, China) containing 100mM glucose was used to dilute tunicamycin dissolved in dimethylsulphoxide (DMSO) (D103272, Aladdin, Shanghai, China). 12 hours after injection, they were anesthetized and sacrificed for harvesting liver tissue.

value: 8 weeks

tag: treatment

value: tunicamycin-injected mice

value: liver


title: PIT_P7-PIT_P8-D5-AD008

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: ob_ob_HFD_2_Hi_S11

value: Hi


title: MBL_sc05_A4

description: single cell RRBS

source_name: blood

value: MBL


title: Liver-Tuni-2


title: MBL_sc05_A3

description: single cell RRBS


title: ob_ob_HFD_2_He_S11

value: He


title: ob_ob_HFD_3_He_S12


title: PIT_P5-PIT_P6-D11-AD002


title: MBL_sc05_A2

description: single cell RRBS


title: PIT_P5-PIT_P6-C12-AD007


title: PIT_P3-PIT_P4-B5-AD010


title: MBL_sc05_B3

description: single cell RRBS


title: Input_Halo_24h

city: Philadelphia

first: Jing

last: Luan

address: 3615 Civic Center Blvd, ARC 315

institute: University of Pennsylvania

data_processing:
Bowtie 1.1.0 was used to align sequences (Langmead and Salzberg, 2012) to the mm9 reference genome. Reads with more than one mismatch or multiple alignments were excluded.
Significantly enriched regions were called using MACS2 version 2.1.0 (Y. Zhang et al., 2008) with the following parameters: P = 10−5, extsize = 300 and local lambda = 100,000 using whole-cell extract input controls.
Reads for the bigwigs were RPM normalized.
Genome_build: mm9

source_name: CTCF-AID-HaloTag+TIR

growth_protocol: G1E-ER4 (Weiss et al., 1997) derived single-cell clones were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with indicated antibodies.
ChIP-seq libraries were prepared using Illumina’s TruSeq ChIP sample preparation kit (Illumina, catalog no. IP-202-1012) according to manufacturer’s specifications, with the addition of size selection (left side at 0.9x, right side at 0.6x) using SPRIselect beads (Beckman Coulter, catalog no. B23318). Library size was determined (average 351 bp, range 333-372 bp) using the Agilent Bioanalyzer 2100, followed by quantitation using real-time PCR using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Libraries were then pooled and sequenced (1x75bp) on the Illumina NextSeq 500 platform according to manufacturer’s instructions. Bclfastq2 v 2.15.04 (default parameters) was used to convert reads to fastq.

treatment_protocol: Cells were treated with either auxin (1mM), Triptolide (1uMx5h) or DRB (75uMx7h). See Description column for Samples.

value: ES-derived erythroid progenitor cells

tag: chip antibody

value: input

value: Input for 24h auxin groups (HaloTag)


title: Liver-Tuni-1


title: sh_3

city: Jinan

first: Tianli

last: Chen

state: Shandong

address: 107 West Wenhua Road

department: Department of General Surgery

institute: Qilu Hospital of Shandong University

description:
WDR5 knockdown shRNA
WDR5_RNA-seq_count.txt

data_processing:
Illumina Casava1.7 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
The transcript abundances(read counts) were estimated with StringTie,software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Raw read counts were normalized and DEG were estimated using R package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements(read counts)

source_name: human cholangiocarcinoma cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WDR5-knockdown shRNA


title: C3H10T1-2_Setd2KO_H3K27me3

first: Chao

last: Lu

state: New York

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

data_processing:
Basecalls performed using Illumina CASAVA version 1.7
For ATAC-seq, ChIP-seq and RNA-seq samples, Reads were aligned to the mm10 genome assembly using HISAT2 version 2.1.0 using default parameters
For ChIP-seq samples, ChIP-Rx normalization was performed according to Weinberg et al., Nature, 2019
For RNA-seq samples, 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.
For WGBS samples, Reads were aligned to the mm10 genome assembly using BWA version 0.6.1 after converting the reference  genome to bisulfite mode
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools
Supplementary_files_format_and_content: tdf files were generated using IGVtools
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Rx libraries were prepared according to Weinberg et al., Nature, 2019.

value: embryo

value: fibroblast

tag: cell line

tag: genotype/variation


title: C3H10T1-2_Nsd1-2KO_H3K27me3


title: PIT_P5-PIT_P6-G9-AD008

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
The snmC-seq2 protocol was applied to individual nuclei isolated from pituitary pooled from 30 adult male C57BL/6 mice
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: Pituitary


title: MBL_sc05_A1

description: single cell RRBS

data_processing:
Bulk RRBS processing: Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.05 -s 16 -w 100 -S 1 -R -u -m 0. Methylation rates were called using custom scripts and subsequently filtered for coverage (min 10).
Single cell processing: Adapter clipping and quality trimming using cutadapt. Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.1 -s 12 -q 20 -w 100 -S 1 -R -u -m 0. Methylation rates were called using mcall.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file from coverage filtered Bed file (<chr> <start> <end> <methylation rate>)

extract_protocol:
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.

value: MBL 05

value: pre-treatment


title: C3H10T1-2_H3K36M_H3K36me2


title: C3H10T1-2_H3K36M_H3K27me3


title: sh_2

tag: transfection


title: Input_5T

source_name: CTCF-AID-mCherry+TIR

tag: cell type

value: Input for 6h auxin groups


title: PIT_P5-PIT_P6-A9-AD006


title: Input_7D

value: Input for 24h auxin groups


title: Liver-Ctrl-2

source_name: liver from vehicle-injected mice

value: 8 weeks

value: vehicle-injected


title: Liver-Ctrl-3

value: liver


title: Liver-Ctrl-1


title: PIT_P7-PIT_P8-H6-AD002

value: male


title: Input_24h

value: Input for 7h DRB groups


title: CKD2 [RNA-Seq]

city: BEIJING

first: YINGCHUN

last: HAN

state: BEIJING

address: CHAOYANG DISTRICT

institute: Anzhen Hospital

data_processing:
Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2 , which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes
Genome_build: Mus_musculus.GRCm38.89
Supplementary_files_format_and_content: FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes

source_name: aorta

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Four samples were pooled into one sample for miRNA sequencing at each time-point. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, 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. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed

treatment_protocol: Mice (8 weeks old) were anesthetized with 1% pentobarbital sodium (100mg/kg) and two poles of the left kidney were removed. Mice were allowed to recover for 1 week, then anesthetized for removal of the right kidney. Mice were fed a diet containing 2% phosphate and water containing 0.45% NaCl for 4 weeks to induce medial calcificaiton(CKD group). ApoE knockout mice were fed a chow diet for 16 months to form atherosclerotic calcifications(ApoE group). 8-week wild type mice were used for control(Ctrl group).

value: aorta

value: chronic kidney diseased (medial calcification)


title: CKD1 [RNA-Seq]


title: scr_3

description:
scramble shRNA
WDR5_RNA-seq_count.txt

value: scramble shRNA


title: sh_1


title: PIT_P1-PIT_P2-G11-AD002


title: Input_18h

value: ES-derived erythroid progenitor cells

value: input

value: Input for 5h Triptolide groups


title: Input_Halo_0h

value: Input for No-treatment groups (HaloTag)


title: ApoE2

value: ApoE-/-(atherosclerotic calcificaiton)


title: scr_2

description:
scramble shRNA
WDR5_RNA-seq_count.txt


title: Input_12h


title: scr_1

description:
scramble shRNA
WDR5_RNA-seq_count.txt


title: ApoE1


title: PIT_P7-PIT_P8-B2-AD004

value: Pituitary


title: PIT_P1-PIT_P2-C6-AD010


title: Ctrl2

value: wild type


title: PIT_P1-PIT_P2-D11-AD006


title: Input_4h

value: Input for 4h auxin groups


title: Input_6h

value: Input for 6h auxin groups


title: Ctrl1


title: E008

city: Shanghai

first: Haoyan

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg38) using HISAT2 version 2.1.0   with the default options with a TopHat transcript index built from Ensembl_GRCh38.
Count files of the aligned sequencing reads were generated by the featurecount
Genome_build: hg38
Supplementary_files_format_and_content: count file

source_name: human colorectal cancer tissue

extract_protocol:
Total RNA of colorectal tissues was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human colorectal cancer tissue

tag: passage


title: Input_0h

value: Input for No-treatment groups


title: E021


title: PIT_P7-PIT_P8-G10-AD006

tag: tissue


title: E019


title: PIT_P1-PIT_P2-H2-AD007


title: CKD2

data_processing:
Raw Data was processed with in-house scripts. The filtering criteria was as follows:1) Remove the reads without 3’adapter 2) Remove the reads without insert fragment 3) Remove the reads contain too much A/T 4) Remove the reads which length is out of range 5) Remove the low-quality reads
Using Bowtie1 to build the reference genome index, and then mapping the clean reads to the genome. Bowtie1 is fast and accurate, and has good perfor ming in short reads alignment.
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/m RNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
After got the count of mature miRNA in miRDeeo2, TPM（ Transcripts Per Million）was used for estimation and normalization.
Genome_build: Mus_musculus.GRCm38.89
Supplementary_files_format_and_content: TPM（ Transcripts Per Million）was used for estimation and normalization.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Four samples were pooled into one sample for miRNA sequencing at each time-point. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Total RNA was separated by 15% agarose gels to extract the small RNA (18-30 nt). After precipitated by ethanol and centrifugal enrichment of small RNA sample, the library was prepared according to the method and process of Small RNA Sample Preparation Kit (Illumina, RS-200-0048). The main contents are as follows: 1) Connecting the 3' adaptor to the separated small RNA. 2) Connecting the 5' adaptor to the separated small RNA. 3) RT－PCR. 4) Recycling strips of 145-160bp (22-30nt RNA).

treatment_protocol: Mice were anesthetized and two poles of the left kidney were removed. Mice were allowed to recover for 1 week, then anesthetized for removal of the right kidney. Mice were fed a diet containing 2% phosphate and water containing 0.45% NaCl for 4 weeks after nephrectomy.

value: aortas

tag: protocol

value: CKD


title: CTCF.Halo_24h_ChIPseq_Rep2

value: Millipore 07-729

value: 24h auxin


title: CKD1

tag: age


title: E170


title: Sham2

tag: strain

value: Sham


title: PIT_P5-PIT_P6-B5-AD004

tag: Sex

value: male


title: E155


title: CTCF.Halo_24h_ChIPseq_Rep1

value: ES-derived erythroid progenitor cells


title: CTCF.Halo_0h_ChIPseq_Rep2

value: No treatment


title: E153


title: PIT_P5-PIT_P6-F12-AD007


title: Sham1


title: CTCF.Halo_0h_ChIPseq_Rep1


title: PIT_P3-PIT_P4-D10-AD002


title: E129


title: 50_ng_U018_SR

city: South San Francisco

first: Rajat

last: Bhatnagar

address: Two Tower Place, Suite 940

institute: Verge Genomics

description: pool of RNA from 10 different human cancer cell lines

data_processing:
Reads were aligned with STAR version 2.7.2  to the reference genome GRCh38 with Ensembl gene annotations. We required genes to have a minimum 3 counts per million in at least 20% of samples. Genes not satisfying this requirement were removed.  After filtering, approximately 12,000 genes remained.  To compare absolute gene expression, reads were normalized via the regularized log transform.
Genome_build: GRCh38

source_name: Universal Human Reference RNA (UHRR)

extract_protocol:
1. Swift RNA Library Prep. 100, 50 and 10 ng of UHRR was used as direct input for NEBNext Ploy(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490). In the final elution step, mRNA was eluted off the beads into the Swift RNA Library Kit Fragmentation Buffer. Libraries were prepared and indexed (Swift Unique Dual Indexing Kit, X9096) using Swift recommended protocol. cDNA libraries were diluted 1:5 in low TE buffer and analyzed on Agilent 4200 TapeStation using D5000 HS DNA screentape. Libraries that gave yields < 4 nM were amplified using the Swift Library Amplification Primer Kit (88196).
2. Swift Rapid RNA Library Prep. 200, 100 and 50 ng of UHRR was used as direct input for NEBNext Ploy(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490). In the final elution step, mRNA was eluted off the beads into the Swift RNA Library Kit Fragmentation Buffer. Libraries were prepared and indexed (Swift Unique Dual Indexing Kit, X9096) using Swift recommended protocol. cDNA libraries were diluted 1:1 in low TE buffer and analyzed on Agilent 4200 TapeStation using D5000 DNA screentape.
3. Illumina TruSeq Stranded mRNA Library Prep. 500, 200, 100 and 50 ng of UHRR was used as direct input for the Illumina TruSeq Stranded mRNA (20020594). Libraries were prepared and indexed (IDT for Illumina-TruSeq RNA UD Indexes, 20022371) as outlined in the TruSeq Stranded mRNA Reference Guide.

value: Adenocarcinoma (mammary gland), Melanoma, Hepatoblastoma (liver), Liposarcoma, Adenocarcinoma (cervix), Histiocytic lymphoma (macrophage; histocyte), Embryonal carcinoma (testis), Lymphoblastic leukemia(T lymphoblast), Glioblastoma (brain), Plasmacytoma/myeloma (B lymphocyte)

tag: commercial source

value: ThermoFisher (QS0639)

tag: method

value: Swift Rapid library prep


title: E128


title: Rad21_0h_ChIPseq_Rep3

value: Abcam Ab992


title: 50_ng_U017_SR


title: PIT_P5-PIT_P6-G11-AD012

first: Joseph

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: Pituitary


title: 50_ng_U016_SR


title: Rad21_0h_ChIPseq_Rep2


title: 50_ng_U010_S

value: Swift library prep


title: Rad21_0h_ChIPseq_Rep1


title: E012


title: CTCF_7D_ChIPseq_Rep2

value: 7h DRB


title: PIT_P3-PIT_P4-F10-AD004


title: PIT_P3-PIT_P4-B8-AD001


title: 50_ng_U009_S


title: CTCF_7D_ChIPseq_Rep1


title: 50_ng_U008_S


title: CTCF_5T_ChIPseq_Rep2

value: 5h Triptolide


title: 50_ng_U007_S


title: PIT_P7-PIT_P8-D3-AD008


title: CTCF_5T_ChIPseq_Rep1


title: 50_ng_U006_S


title: PIT_P5-PIT_P6-G4-AD001


title: PIT_P5-PIT_P6-F4-AD008


title: E120

value: human colorectal cancer tissue


title: PIT_P3-PIT_P4-E4-AD004


title: CTCF_24h_ChIPseq_Rep2


title: CTCF_24h_ChIPseq_Rep1


title: 50_ng_U001_SR


title: PIT_P5-PIT_P6-H5-AD010


title: PIT_P7-PIT_P8-F2-AD008


title: 50_ng_A5_IL

value: Illumina library prep


title: PIT_P5-PIT_P6-C12-AD012


title: PIT_P3-PIT_P4-C7-AD007


title: CTCF_18h_ChIPseq_Rep2

value: 18h auxin


title: CTCF_18h_ChIPseq_Rep1

value: Millipore 07-729


title: 50_ng_A4_IL


title: Puretype_5

city: Tokorozawa

first: Kosuke

last: Miyai

state: Saitama

address: Namiki 3-2

department: Basic Pathology

country: Japan

institute: National Defense Medical College

description: Gene expression of pure seminoma

hyb_protocol: 0.6 μμg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μμl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μμl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Pure-type seminoma 5

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μμg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was isolated using the NucleoSpin totalRNA FFPE kit (Macherey-Nagel, Düren, Germany) in accordance with the manufacturer’s instructions. Samples with a minimal concentration of 50 ng/μl and DV200 50% or more, quantified using Agilent RNA 600 Nano kit (Agilent Technologies, Santa Clara, CA) and Agilent 2100 Bioanalyzer (Agilent Technologies), proceeded to further investigation.

treatment_protocol: For each case, we selected formalin-fixed, paraffin-embedded (FFPE) tissue blocks containing the areas in which histological diagnosis of seminoma was performed. These tissue blocks were then cut into 10-μm-thick sections and the tumor areas were manually microdissected into microcentrifuge tubes. The area of the cells microdissected from a single slide section typically ranged from 5 to 10 mm2.

value: Pure-type seminoma

tag: tissue preparation

value: FFPE block of resected tissue


title: Puretype_4

description: Gene expression of pure seminoma

source_name: Pure-type seminoma 4


title: CTCF_12h_ChIPseq_Rep2

value: 12h auxin


title: PIT_P3-PIT_P4-C9-AD004

city: La Jolla

last: Ecker

value: male


title: 50_ng_A3_IL


title: PIT_P3-PIT_P4-D7-AD004


title: Puretype_6

description: Gene expression of pure seminoma

source_name: Pure-type seminoma 6


title: CTCF_12h_ChIPseq_Rep1

value: ES-derived erythroid progenitor cells


title: 50_ng_A2_IL

value: Adenocarcinoma (mammary gland), Melanoma, Hepatoblastoma (liver), Liposarcoma, Adenocarcinoma (cervix), Histiocytic lymphoma (macrophage; histocyte), Embryonal carcinoma (testis), Lymphoblastic leukemia(T lymphoblast), Glioblastoma (brain), Plasmacytoma/myeloma (B lymphocyte)


title: 50_ng_U002_SR

value: ThermoFisher (QS0639)


title: PIT_P1-PIT_P2-H12-AD008


title: CTCF_6h_ChIPseq_Rep2

value: 6h auxin


title: Puretype_1

description: Gene expression of pure seminoma

source_name: Pure-type seminoma 1


title: Mixedtype_6

description: Gene expression of mixed seminoma

source_name: Mixed-type seminoma 6

value: Mixed-type seminoma


title: Mixedtype_4

description: Gene expression of mixed seminoma

source_name: Mixed-type seminoma 4


title: PIT_P5-PIT_P6-B1-AD010

value: Pituitary


title: Mixedtype_5

description: Gene expression of mixed seminoma

source_name: Mixed-type seminoma 5


title: 500_ng_B8_IL


title: PIT_P1-PIT_P2-C1-AD002

source_name: C57BL/6J Male P56 Mouse Brain


title: CTCF_6h_ChIPseq_Rep1


title: CTCF_4h_ChIPseq_Rep2

value: 4h auxin


title: Puretype_2

description: Gene expression of pure seminoma

source_name: Pure-type seminoma 2


title: Mixedtype_3

description: Gene expression of mixed seminoma

source_name: Mixed-type seminoma 3


title: 500_ng_B7_IL


title: PIT_P7-PIT_P8-D2-AD008


title: Mixedtype_2

description: Gene expression of mixed seminoma

source_name: Mixed-type seminoma 2


title: KI600: Input in Lung at E14.5

city: CHICAGO

first: Jeffrey D.

last: Steimle

state: IL

address: 900 E. 57th Street, KCBD 5240

institute: University of Chicago

data_processing:
Raw sequencing reads were aligned to the mm10 genome using Bowtie2 (Langmead and Salzberg 2012, Nat Methods) and SAMtools (Li et al 2009 Bioinformatics, Li 2011 Bioinformatics) requiring a minimum mapping quality of 40 (-q 40).
Pooled peak calling was performed using default settings of MACS2 callpeak (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc) with a q-value set to 0.05 (-q 0.05).
A fold-enrichment track was generated using MACS2 using the bdgcmp function (-m FE) for visualization on the genome browser (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc).
Peaks overlapping ENCODE blacklist sites (Amemiya et al. 2019; ENCODE Project Consortium 2012) were removed from the final set of peaks.

source_name: Heart

extract_protocol:
To prepare chromatin extract, micro-dissected tissue from E14.5 CD-1 mouse embryos (1 whole lung per replicate) obtained from Charles River were cross-linked in PBS containing 1% formaldehyde at 25°C for 10 minutes. The reaction was quenched by 125 mM glycine. The cross-linked tissues were
incubated in LB1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton X-100) with protease and phosphatase inhibitors on ice for 10
minutes. The tissues were then sonicated in LB3 (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1% Triton X-100)
with protease and phosphatase inhibitors. Chromatin extract was then cleared by centrifugation at 14,000g, 4°C for 10 minutes. For immunoprecipitation, the chromatin extract was incubated with 5ug of the anti-TBX5 antibody (Santa Cruz Biotechnology sc-17866; Lot #G1516) at 4°C for >12 hours in a total volume of 200 μL. The immune-complexes were captured by Protein G-conjugated magnetic beads (Life Technologies, 1003D), washed in sequence by LB3, LB3 with 1 M NaCl, LB3 with 0.5 M NaCl, LB3, and TE (10 mM Tris-HCl, pH 8.0; 1 mM EDTA). The captured chromatin was eluted in ChIP Elution Buffer (10 mM TrisHCl, pH 8.0; 1 mM EDTA; 1% SDS; 250 mM NaCl) at 65°C. After RNase and proteinase K treatment and reverse cross-linking, DNA were purified.


title: 500_ng_B6_IL


title: Mixedtype_1

description: Gene expression of mixed seminoma

source_name: Mixed-type seminoma 1


title: KI595: Tbx5 ChIP in Lung at E14.5

source_name: Lung


title: KI596: Tbx5 ChIP in Lung at E14.5


title: 500_ng_B5_IL


title: PIT_P1-PIT_P2-H8-AD012


title: CTCF_0h_ChIPseq_Rep1

source_name: CTCF-AID-mCherry+TIR

value: No treatment


title: 50_ng_A1_IL


title: PIT_P7-PIT_P8-F8-AD004


title: 500_ng_B4_IL


title: 200_ng_U024_SR

value: Swift Rapid library prep