title: MG63-3_E9_treated: RNA Pol II ChIP Seq

data_processing:
The FASTX-Toolkit v0.0.13 was used to remove adapter sequences and trim reads with the quality cutoff of 20, excluding any reads shorter than 25bp. ChIP-seq reads were aligned to hg19 with Bowtie 2 v2.0.649, searching for multiple alignments but reporting the one with the best mapping quality score. PCR duplicates were removed using SAMtools 1.2. Peaks were detected with MACS2 2.1.1.20160309 with an input DNA sample as control, scaling the input dataset to match the read depth of the ChIP dataset. MACS2 peaks with a q-value of greater than 0.001 and overlapping ENCODE blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were filtered out. BigWIGs were generated with DeepTools v3.0.1-2-2fa58e8 and normalized to 1x average coverage (RPGC option)
Cutadapt v1.14 was used to trim 3’ adapters, discarding trimmed reads shorter than 20bp. Sickle v1.33 was then used to trim reads with the quality cutoff of 20. RNA-Seq reads were aligned to hg19 assembly plus ERCC RNA Spike-In DNA sequences with STAR v2.5.3a. Cufflinks v2.0.2 was run with genomic bias correction to quantify the levels of transcripts in the hg19 reFLAT annotations file as well as the ERCC transcripts file. Scatter plots of ERCC transcript FPKMs versus their expected concentrations in the spike-in mix were constructed to aid in quality control assessment of the data. The FPKM table was then floored to the background noise level of 0.3. Differential expression analysis between E9-treated and untreated samples was performed by calculating the fold change of mean E9 FPKM over mean DMSO FPKM.
After removing adapter sequences using cutadapt v1.8.1,1 the DNA FASTQ files were aligned to the hg19 reference genome using BWA-mem (v0.7.17-r1188).2,3 The aligned files were then indexed and had PCR duplicates removed using samtools (v0.1.18).4 Each BAM file underwent base quality score recalibration using GATK(v4.0.1.1).5
Refseq hg19 genes underwent the following filtering steps prior to use in downstream analyses for each pair of treated and untreated samples to ensure 1-to-1 mapping of genes to TSS’s: 1:Retrieve RNA-Pol RPKM within 1KB of each TSS and calculate the minimum of E9 and DMSO RPKMs. In case of the same gene with multiple TSS’s, only retain the gene record with the max RNA-Pol RPKM minimum. 2:In case of multiple genes with the same TSS, calculate the minimum FPKM between E9 and DSMO for each gene and only retain the gene with the max FPKM minimum
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq and whole genome sequencing WIG tracks were generated with deeptools v3.1.3 and normalized with the RPGC option

value: RNA Go-ChIP-Grade™ Purified anti-RNA Polymerase II RPB1 Antibody (Biolegend #664911)


title: MG63-3_E9_treated: input DNA

status: Public on Jun 06 2019

type: SRA

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

country: USA

institute: Case Western Reserve University

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: highly metastatic osteosarcoma cell line

growth_protocol: Human osteosarcoma cell lines (MG63.3-GFP, 143B-GFP) were grown in DMEM 1x (Gibco, 11965-092) supplemented with 10% FBS (Corning, 35-010-CV) and 1% penicillin/streptomycin.

extract_protocol:
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared as previously described (Schmidt et al. 2009). For RNA-seq, Total RNA was treated with DNase I (Invitrogen, Carlsbad, CA). RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, Foster City, CA) and analyzed on an Agilent Bioanalyzer 2100 for integrity. PolyA+ RNA was isolated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol. For Whole Genome Sequencing, PCR-free libraries were prepared from MG63.3-GFP and 143B-GFP cells using TruSeq DNA PCR-Free High Throughput Library Prep Kit (Illumina, 20015963) and following the manufacturer’s instructions.

treatment_protocol: For ChIP-seq and RNA-seq, 143B-GFP and MG63.3-GFP cells were treated for 6 hours with E9 at 200nM or DMSO. Cells prepared for ChIP-seq were crosslinked with formalin.

tag: tissue

tag: cell line

tag: chip antibody


title: RA_non treated9__CD4-Tn cells

city: sinjuku-ku

first: Masaru

last: Takeshita

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

country: Japan

institute: Keio University

library_source: transcriptomic

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

molecule: total RNA

source_name: Tn CD4 cell

growth_protocol: Healthy volunteers and rheumatoid arthritis patients

extract_protocol:
Total RNA from were extracted using RNeasy Micro kit (Qiagen).
0.2 or 1 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit. Then cDNA is amplified using Ion AmpliSeq™ technology. After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 75 pM and pooled equally, with eighteen individual samples per pool.

treatment_protocol: Peripheral mononuclear cells were isolated by density gradient centrifugation, and CD4 and CD8 T cell were purified from them using MojoSort (Biolegend). Cells were sorted by FACS Aria Ⅲ. Tn, Tcm, Tem, and Temra cells were defined as CD45RA+CCR7+, CD45RA-CCR7+, CD45RA-CCR7-, and CD45RA+CCR7-, respectively.

value: blood

tag: cell type

value: Tn CD4 cell

tag: disease status

value: RA non treatment

tag: age

tag: gender

value: M


title: 1381425_ZT0-O3-B_S8

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
O3__ZT0
RNA-Seq Stranded mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to dm3 whole genome using an internal pipeline that employs bwa and STAR.
HTSeq was used to extract raw counts.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *_merged.txt: Gene symbols and raw count values in 2-column tab-delimited txt file, one for each sample.

organism: Drosophila melanogaster

source_name: skeletal muscles

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NA, genotype based.

tag: strain

value: Skeletal muscles

tag: time point


title: RA_non treated9__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell


title: MG63-3_E9_treated: CDK12 ChIP Seq

value: highly metastatic osteosarcoma cell line

value: anti-CDK12 (gift from Arno Greenleaf)


title: RA_non treated8__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell

value: F


title: 1381421_ZT0-O1-A_S4

description:
O1__ZT0
RNA-Seq Stranded mRNA


title: MG63-3_DMSO_treated: input DNA


title: MG63-3_E9_treated: Pol II Ser2 ChIP Seq

value: Anti-RNA polymerase II subunit B1 (phospho CTD Ser-2) Antibody, clone 3E10 (Millipore #04-1571)


title: MG63-3_E9_treated: H3K27ac ChIP Seq

value: rabbit anti-H3K27ac (Abcam no. 4729)


title: RA_non treated8__CD8-Temra cells

source_name: Temra CD8 cell

value: Temra CD8 cell


title: RA_non treated8__CD8-Tem cells

source_name: Tem CD8 cell

value: Tem CD8 cell


title: RA_non treated8__CD8-Tcm cells

source_name: Tcm CD8 cell

value: Tcm CD8 cell


title: RA_non treated8__CD4-Tn cells


title: MG63-3_DMSO_treated: CDK12 ChIP Seq


title: MG63-3_DMSO_treated: Pol II Ser2 ChIP Seq


title: RA_non treated8__CD4-Tem cells

source_name: Tem CD4 cell

value: Tem CD4 cell


title: MG63-3_DMSO_treated: H3K27ac ChIP Seq


title: RA_non treated8__CD4-Tcm cells


title: MG63-3_DMSO_treated: RNA Pol II ChIP Seq

value: RNA Go-ChIP-Grade™ Purified anti-RNA Polymerase II RPB1 Antibody (Biolegend #664911)


title: RA_non treated7__CD8-Tn cells

value: blood


title: RA_non treated7__CD8-Temra cells


title: 143B_E9_treated: RNA Pol II ChIP Seq


title: 143B_E9_treated: input DNA


title: 143B_E9_treated: Pol II Ser2 ChIP Seq


title: RA_non treated9__CD4-Tem cells


title: 143B_E9_treated: CDK12 ChIP Seq


title: 143B_DMSO_treated: input DNA


title: 143B_E9_treated: H3K27ac ChIP Seq


title: RA_non treated7__CD4-Tem cells


title: RA_non treated7__CD8-Tcm cells


title: RA_non treated7__CD4-Tn cells

value: Tn CD4 cell


title: 143B_DMSO_treated: RNA Pol II ChIP Seq


title: RA_non treated6__CD8-Tn cells

value: RA non treatment


title: RA_non treated7__CD4-Tcm cells

value: M


title: 143B_DMSO_treated: CDK12 ChIP Seq


title: RA_non treated6__CD8-Tem cells


title: CRC, primary, T42

city: Nanjing

first: Cheng

last: Wang

address: No. 818 East Tianyuan Road

country: China

institute: Nanjing Medicial University

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA reads were generated, aligned to the GENCODE v19 genome assembly with STAR v2.4.1 and quantified using featureCounts v1.5.0.
The raw read counts were normalized with DESeq2 followed by differential expression analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for all samples

source_name: Colorectal cancer

extract_protocol:
FFPE RNA was extracted using the Wuxi in-house method after FFPE sample sections were scalped into 1.5 mL microcentrifuge tubes, and then deparaffinization solution was used to remove paraffin. The RNA integrity was determined using a 2100 Bioanalyser (Agilent) with DV200 (Percentage of RNA fragments > 200 nt fragment distribution value) and quantified by the NanoDrop (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: patient P2

value: primary colorectal cancer (CRC) tissue


title: RA_non treated6__CD8-Tcm cells


title: RA_non treated6__CD8-Temra cells


title: RA_non treated6__CD4-Tcm cells

value: Tcm CD4 cell


title: RA_non treated6__CD4-Tem cells


title: CRC, primary, T39

value: patient P1


title: RA_non treated6__CD4-Tn cells


title: CRC, metastatic, T41

value: Brain metastatic tissue


title: RA_non treated5__CD8-Tn cells

value: Tn CD8 cell

value: F


title: RA_non treated5__CD8-Tcm cells


title: MDS_26 methylation values

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: Raw data are unavailable for this sample due to data loss.

data_processing:
Library strategy: DREAM
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

source_name: MDS bone marrow

extract_protocol:
Puregene Gentra DNA extraction.
Two to five micrograms of genomic DNA spiked with 2 picograms of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

value: bone marrow

tag: diagnosis

value: MDS


title: Mulitplexed BULK: BM-MNC

city: Seattle

first: Andrew

last: Butler

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

data_processing:
CITE-seq RNA reads were mapped to the human genome (GRCh38). Transcripts were quanitfied using CellRanger v2.1.0
ADT and HTO antibody counts were quantified using CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Cells were demultiplexed after normalization via a centered log ratio transformation using the HTOdemux function in Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data provided as a TSV expression matrix where the rows correspond to genes and the columns to either a particular replicate for the bulk data, or single cells for the single-cell data

source_name: Bone Marrow Mononuclear Cells

growth_protocol: For both bulk and scRNA-seq experiments: BM MNCs were thawed in 37C water bath. RPMI +10% FBS media was added drop-wise to the thawed cells. Cells were spun down and resuspended in PBS 1X. Cell  viability was quantified using trypan blue.

extract_protocol:
For the bulk experiment:  CD4-/CD8+/CD3+CD69+ and  CD4-/CD8+/CD3+CD69- cells were sorted into wells containing RLT lysis buffer using a SONY SH800 sorter. RNA was isolated by performing a 2X Ampure bead cleanup. RNA was resuspended into RT mix and cDNA synthesis and amplification was performed as described in dx.doi.org/10.17504/protocols.io.nkgdctw. Briefly, we used a modified version of Smart Seq 2 protocol that allows for sequencing of the 3' end of each transcript.
For the scRNA/CITE-seq experiment: a panel of 25 antibodies (ADTs) was used to stain the cells according to the CITE-seq protocol. To identify cell doublets, we split cells into 10 aliquots and stained each aliquot with a unique hashing (HTOs) antibody.  Samples were washed and recombined and load on a 10genomics chip. 3prime 10x genomics Version 2 was ran and the manufacturers protocols was followed for cDNA library generation. To recover HTOs and ADTs we followed the CITE-seq protocol found here: https://cite-seq.com/protocol/
CITE-seq (10x genomics 3prime Version 2)


title: RA_non treated5__CD8-Tem cells

value: Tem CD8 cell


title: MDS_23 methylation values


title: MDS_25 methylation values


title: MDS_24 methylation values


title: RA_non treated5__CD4-Tn cells


title: MDS_22 methylation values


title: 143B_DMSO_treated: Pol II Ser2 ChIP Seq

value: highly metastatic osteosarcoma cell line

value: Anti-RNA polymerase II subunit B1 (phospho CTD Ser-2) Antibody, clone 3E10 (Millipore #04-1571)


title: MDS_21 methylation values


title: RA_non treated5__CD4-Tcm cells


title: RA_non treated5__CD4-Tem cells

value: Tem CD4 cell


title: 143B_DMSO_treated: H3K27ac ChIP Seq

value: rabbit anti-H3K27ac (Abcam no. 4729)


title: MDS_20 methylation values


title: RA_non treated4__CD8-Temra cells

value: blood

value: Temra CD8 cell


title: RA_non treated4__CD8-Tn cells

value: RA non treatment


title: MDS_19 methylation values


title: CRC, metastatic, T40


title: MDS_18 methylation values


title: RA_non treated4__CD8-Tem cells


title: RA_non treated4__CD8-Tcm cells

value: Tcm CD8 cell


title: RA_non treated4__CD4-Tn cells

value: Tn CD4 cell


title: MDS_15 methylation values


title: MDS_16 methylation values


title: RA_non treated4__CD4-Tcm cells

value: Tcm CD4 cell


title: RA_non treated3__CD8-Tn cells


title: MDS_14 methylation values


title: RA_non treated3__CD8-Temra cells


title: MDS_12 methylation values


title: MDS_11 methylation values


title: MDS_13 methylation values


title: RA_non treated3__CD4-Tn cells


title: RA_non treated3__CD4-Tem cells


title: MDS_10 methylation values


title: RA_non treated3__CD4-Tcm cells


title: RA_non treated2__CD8-Tn cells


title: RA_non treated2__CD8-Temra cells


title: MDS_09 methylation values


title: RA_non treated2__CD8-Tem cells


title: RA_non treated2__CD8-Tcm cells


title: MDS_05 methylation values


title: MDS_17 methylation values


title: MDS_04 methylation values


title: RA_non treated2__CD4-Tn cells


title: MDS_03 methylation values


title: RA_non treated2__CD4-Tem cells


title: MDS_02 methylation values


title: MDS_01 methylation values


title: RA_non treated10__CD8-Tn cells


title: AML_83  methylation values

source_name: AML bone marrow

value: AML


title: AML_74 methylation values


title: AML_82 methylation values


title: RA_non treated10__CD8-Tem cells


title: RA_non treated10__CD8-Temra cells


title: AML_69 methylation values


title: RA_non treated10__CD4-Tn cells


title: MDS_08 methylation values


title: MDS_07 methylation values


title: AML_60 methylation values


title: AML_56 methylation values


title: RA_non treated1__CD8-Temra cells


title: RA_non treated10__CD4-Tem cells


title: RA_non treated1__CD8-Tem cells


title: RA_non treated1__CD8-Tn cells


title: RA_non treated10__CD4-Tcm cells


title: AML_Z  methylation values

tag: Sex

value: M

tag: age years


title: AML_W rep2 methylation values


title: RA_non treated1__CD4-Tn cells


title: AML_X methylation values


title: AML_Y methylation values


title: RA_non treated2__CD4-Tcm cells


title: RA_non treated1__CD4-Tcm cells


title: RA_MTX treated9__CD8-Tn cells

value: Tn CD8 cell

value: RA MTX treatment


title: RA_non treated10__CD8-Tcm cells

value: F


title: RA_MTX treated9__CD8-Temra cells


title: AML_V rep1 methylation values

value: bone marrow


title: AML_U methylation values


title: AML_T methylation values


title: RA_MTX treated9__CD8-Tcm cells


title: RA_MTX treated9__CD8-Tem cells

value: Tem CD8 cell


title: RA_MTX treated9__CD4-Tn cells


title: AML_R methylation values


title: AML_P methylation values


title: AML_Q methylation values


title: RA_non treated1__CD4-Tem cells


title: RA_MTX treated8__CD8-Tn cells


title: RA_MTX treated9__CD4-Tem cells


title: AML_N methylation values


title: AML_W rep1 methylation values


title: AML_M methylation values


title: AML_O methylation values


title: RA_MTX treated9__CD4-Tcm cells


title: AML_L methylation values


title: RA_MTX treated8__CD8-Tcm cells


title: RA_MTX treated8__CD8-Tem cells


title: AML_V rep2 methylation values


title: AML_J methylation values


title: AML_K methylation values


title: RA_MTX treated8__CD8-Temra cells


title: RA_MTX treated8__CD4-Tem cells


title: RA_MTX treated8__CD4-Tcm cells


title: AML_I methylation values


title: RA_MTX treated7__CD8-Temra cells


title: AML_H methylation values


title: RA_MTX treated8__CD4-Tn cells


title: AML_G methylation values


title: RA_MTX treated7__CD8-Tem cells


title: AML_F methylation values


title: RA_MTX treated7__CD8-Tcm cells


title: AML_E methylation values


title: AML_S methylation values


title: AML_E99 methylation values


title: RA_MTX treated6__CD8-Tn cells


title: RA_MTX treated7__CD4-Tn cells


title: AML_E96 methylation values


title: AML_E95 methylation values


title: RA_MTX treated6__CD8-Temra cells


title: AML_E94 methylation values


title: RA_MTX treated6__CD8-Tcm cells


title: AML_E92 methylation values


title: RA_MTX treated6__CD4-Tem cells


title: RA_MTX treated6__CD4-Tn cells


title: AML_E98 methylation values


title: RA_MTX treated6__CD4-Tcm cells


title: AML_E91 methylation values


title: AML_E90 methylation values


title: AML_E8 methylation values


title: RA_MTX treated5__CD8-Tem cells


title: RA_MTX treated5__CD8-Tn cells


title: AML_E88 methylation values


title: RA_MTX treated7__CD4-Tcm cells


title: RA_MTX treated5__CD4-Tcm cells


title: AML_E85 methylation values


title: AML_E82 methylation values


title: AML_E84 methylation values


title: RA_MTX treated5__CD4-Tn cells


title: RA_MTX treated7__CD4-Tem cells


title: RA_MTX treated6__CD8-Tem cells


title: RA_MTX treated4__CD8-Tn cells


title: AML_E75 rep1 methylation values


title: AML_E75 rep2 methylation values


title: AML_E79 methylation values


title: RA_MTX treated4__CD8-Tcm cells


title: RA_MTX treated4__CD4-Tn cells


title: RA_MTX treated4__CD8-Tem cells


title: RA_MTX treated4__CD4-Tem cells


title: AML_E72 methylation values


title: AML_E78 methylation values


title: RA_MTX treated3__CD8-Temra cells


title: RA_MTX treated3__CD8-Tem cells


title: RA_MTX treated5__CD4-Tem cells


title: RA_MTX treated4__CD4-Tcm cells


title: AML_E69 methylation values


title: AML_E65 methylation values


title: RA_MTX treated3__CD4-Tem cells


title: RA_MTX treated3__CD4-Tcm cells


title: AML_E66 methylation values


title: AML_E80 methylation values


title: RA_MTX treated3__CD4-Tn cells


title: AML_E64 methylation values


title: AML_E62 methylation values


title: AML_E63 methylation values


title: RA_MTX treated2__CD8-Tn cells


title: RA_MTX treated2__CD8-Tem cells


title: AML_E61 methylation values


title: RA_MTX treated2__CD8-Tcm cells


title: AML_E60 methylation values


title: AML_E70 methylation values


title: AML_E71 methylation values


title: RA_MTX treated10__CD8-Tn cells


title: AML_E58 methylation values


title: RA_MTX treated2__CD4-Tcm cells


title: RA_MTX treated2__CD4-Tem cells


title: AML_E54 methylation values


title: RA_MTX treated2__CD4-Tn cells


title: AML_E5 methylation values


title: RA_MTX treated10__CD8-Temra cells


title: AML_E56 methylation values


title: AML_E52 methylation values


title: AML_E50 methylation values


title: HACAT_treated_rep3

city: Munich

first: Julia

last: Philippou-Massier

state: Bavaria

address: Feodor-Lynen-Strasse 25

department: Gene Center

country: Germany

institute: LMU

description: Analysis of polyadenylated transcripts by Next Generation Sequencing

data_processing:
Basecalling from raw image files was done by RTA 1.18.66.3 (Illumina) and sequence data were stored in fastq format.
Demultiplexing was done using a custom Demultiplex tool allowing one mismatch in barcode sequence.
Mapping: Demultiplexed sequences were mapped against the human genome (hg19) with RNA-STAR Mapper (v.2.5.2b).
The number of reads were counted using HTSeq-count with union mode grouped by gene_id. Read counts were normalized with DESeq2 (v.1.0.19) and differential abundances were calculated with an adj. p-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: HTseqCount_all: tab seprated file. Data in this file was processed by using HTSeq-count and grouped by genes.

source_name: skin/epidermis

growth_protocol: HaCaT and A431 cells were incubated in DMEM supplemented with 10% fetal calf serum (FCS) (Biochrom) and 1% streptomycin/penicillin (Biochrom) in an incubator (Thermo Fisher Scientific, Munich, Germany) at 37°C with 5% CO2, untill 80% confluence.

extract_protocol:
RNA was isolated using the Direct-zol RNA mini Prep kit (Zymo Research). Therefore a Trizol-Lysat (Invitrogen) of 2 mio harvested cells of each condition was used as input. Isolated RNA was quantified and quality controlled by using a NanoDrop and Bioanalyzer respectivly. Before sequencing library generation, 1 µg of isolated RNA was additionally purified using Agencourt RNAClean XP beads.
Following quantification by NanoDrop and quality control by Bioanalyzer, 500 ng high quality RNA (RIN > 7,5) were used to generate sequencing libraries using the SENSE mRNA-Seq Lib Prep Kit V2 (Lexogen).
Libraries consist only of polyadenylated transcripts.

treatment_protocol: 80 % confluent HaCaT cells were incubated for 24 h with the CM obtained from the cultivation of A431 cells.

value: HACAT

tag: morphology

value: keratinocyte

tag: disease

value: normal

tag: agent

value: CM


title: FigS4B_26415_t20_WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC and trimming of reads was carried out using fastx_trimmer
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: bigwig files

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: sac_cer strain

tag: can_gla strain

tag: antibody

value: none (input)

tag: timepoint

value: Arrested in G2 (Nocodazole)


title: AML_E4 methylation values

tag: tissue


title: FigS4B_26415_t20_IP

value: anti-PK antibody (Bio-Rad)


title: FigS4B_26415_t0_IP


title: RA_MTX treated10__CD4-Tem cells

value: blood

tag: cell type

value: Tem CD4 cell

tag: disease status


title: RA_MTX treated10__CD4-Tcm cells

value: Tcm CD4 cell

tag: age

tag: gender


title: AML_E47 methylation values

value: AML


title: FigS4B_26415_t0_WCE


title: FigS4B_26414_t20_WCE


title: HACAT_treated_rep1

tag: cell line


title: AML_E42 methylation values


title: HACAT_ctrl_rep3


title: RA_MTX treated2__CD8-Temra cells

value: Temra CD8 cell


title: HACAT_ctrl_rep2


title: AML_E40 methylation values

value: M


title: RA_MTX treated1__CD8-Tn cells

value: Tn CD8 cell

value: RA MTX treatment


title: RA_MTX treated10__CD4-Tn cells

value: Tn CD4 cell

value: F


title: HACAT_treated_rep2

value: HACAT


title: FigS4B_26414_t0_WCE


title: RA_MTX treated1__CD4-Tn cells


title: RA_MTX treated10__CD8-Tem cells

value: Tem CD8 cell


title: AML_E39 methylation values

value: bone marrow


title: RA_MTX treated1__CD4-Tcm cells


title: HACAT_ctrl_rep1

value: keratinocyte

value: normal


title: FigS2D_27570_WCE

value: none (input)

value: Arrested in late G1 (Gal-sic1)


title: FigS4B_26414_t0_IP

value: anti-PK antibody (Bio-Rad)

value: Arrested in G2 (Nocodazole)


title: A431_treated_rep3

value: epithelial

value: epidermoid carcinoma

value: CM


title: AML_E34 methylation values

value: AML


title: A431_treated_rep2


title: RA_IFX treated9__CD8-Tn cells

value: blood

value: Tn CD8 cell

value: RA IFX treatment


title: FigS2D_27570_IP


title: FigS2D_27569_WCE


title: A431_treated_rep1


title: FigS4B_26414_t20_IP


title: FigS2D_27569_IP


title: AML_E31 methylation values

value: F


title: RA_IFX treated9__CD8-Tem cells


title: AML_E25 methylation values


title: AML_E3 methylation values

value: M


title: A431_ctrl_rep3


title: Fig5E_27169_t20_WCE

value: cdc45 depletion


title: RA_IFX treated9__CD8-Tcm cells

value: Tcm CD8 cell


title: A431_ctrl_rep2


title: A431_ctrl_rep1


title: AML_E22 methylation values

value: bone marrow


title: Fig5E_27169_t20_IP


title: RA_IFX treated9__CD4-Tn cells

value: Tn CD4 cell


title: Fig5E_27169_t0_WCE

value: none (input)


title: AML_E23 methylation values


title: RA_IFX treated9__CD4-Tem cells

value: Tem CD4 cell


title: Fig5E_27169_t0_IP

value: anti-PK antibody (Bio-Rad)


title: AML_E21 methylation values


title: RA_IFX treated9__CD8-Temra cells

value: Temra CD8 cell


title: AML_E32 methylation values


title: AML_E20 methylation values


title: Fig5E_27168_t20_WCE


title: RA_IFX treated8__CD8-Tn cells


title: AML_E18 methylation values


title: RA_IFX treated8__CD8-Temra cells


title: Fig5E_27168_t20_IP


title: AML_E15 methylation values


title: Fig5E_27168_t0_WCE


title: RA_IFX treated8__CD8-Tem cells

value: Tem CD8 cell


title: RA_IFX treated9__CD4-Tcm cells

value: Tcm CD4 cell


title: Fig5D_24738_t20_WCE

value: Arrested in G2 (Nocodazole)


title: AML_E12 methylation values

value: AML


title: RA_IFX treated8__CD8-Tcm cells

value: blood


title: Fig5E_27168_t0_IP


title: AML_E11 methylation values


title: RA_IFX treated8__CD4-Tn cells


title: Fig5D_24738_t20_IP


title: Kideny_CPS_rep6

type: RNA

city: Valdivia

first: Carlos

last: Spichiger

state: Región de los Rios

address: Instituto de Bioquímica y Microbiología, campus Isla Teja, UACh

department: Instituto de Bioquímica y Microbiología

country: Chile

institute: Universidad Austral de Chile

hyb_protocol: 3,8 µg of fragmented labeled ss cDNA were hybridized to Affymetrix Rat Gene 2.1 ST Array Plates.

scan_protocol: For hybridization, washing, staining and scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

data_processing: All array data were normalized using robust multiarray average (RMA) with GeneChip Expression Console software of Affymetrix.

label: biotin

organism: Rattus norvegicus

source_name: fetal kidney at e19 CPS gestation

label_protocol: In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: At 70-80 days of age (250-300 g) rat females with water and food ad libitum, with 12:12 h photoperiod were mated and the day zero of gestation (E0) was determined by positive sperm in the vaginal smears.

extract_protocol: SV total RNA extraction kit of Promega was used according to the manufacturer's instructions.

treatment_protocol: Pregnant females at E0 were kept in individual cages and separated randomly into two groups: LD group, pregnant females kept 12:12 h photoperiod throughout gestation, and the second group CPS (Chronic photoperiod shifting) corresponding to pregnant females kept under a rotation scheme of photoperiod. At 19th gestation day,  mothers of both groups were euthanizated, fetal kidneys were disected and pooled from 6 fetuses of each -CPS or LD- mother respectively at 08:00 hours clock time.

value: kidney

value: 19 days of gestation

tag: clock time tissue disection


title: RA_IFX treated8__CD4-Tem cells

value: RA IFX treatment

value: F


title: AML_E117 methylation values

tag: diagnosis


title: Kideny_CPS_rep4


title: Kideny_CPS_rep5


title: Fig5D_24738_t0_WCE


title: RA_IFX treated8__CD4-Tcm cells


title: AML_E116 methylation values

tag: Sex


title: RA_IFX treated7__CD8-Tn cells

value: Tn CD8 cell


title: Kideny_CPS_rep1


title: AML_E112 methylation values

value: M

tag: age years


title: Kideny_CPS_rep2


title: AML_E14 methylation values

value: bone marrow


title: Kideny_CPS_rep3


title: Kidney_LD_rep5

source_name: fetal kidney at e19 LD gestation


title: RA_IFX treated7__CD8-Temra cells


title: Fig5D_24697_t20_IP


title: AML_E111 methylation values


title: Fig5D_24697_t0_WCE


title: Fig5D_24697_t20_WCE


title: Kidney_LD_rep3


title: Kidney_LD_rep4


title: RA_IFX treated7__CD4-Tn cells

value: Tn CD4 cell


title: RA_IFX treated7__CD8-Tcm cells

value: Tcm CD8 cell


title: Fig5D_24738_t0_IP


title: Fig5D_24697_t0_IP


title: Kidney_LD_rep6


title: RA_IFX treated7__CD4-Tem cells

value: Tem CD4 cell


title: AML_E110 methylation values


title: Kidney_LD_rep1


title: RA_IFX treated7__CD4-Tcm cells


title: AML_E102 methylation values


title: Fig5A_25947_t20_WCE

value: none (input)


title: Kidney_LD_rep2


title: Fig5A_25947_t20_IP

value: anti-PK antibody (Bio-Rad)


title: AML_D methylation values


title: RA_IFX treated6__CD8-Tn cells


title: Fig5A_25947_t0_WCE


title: AML_E103 methylation values


title: RA_IFX treated6__CD8-Temra cells

value: Temra CD8 cell


title: AML_C methylation values


title: RA_IFX treated6__CD8-Tem cells

value: Tem CD8 cell


title: AML_B methylation values


title: Fig5A_24709_t20_WCE

value: Arrested in G2 (Nocodazole)


title: Fig5A_25947_t0_IP


title: AML_A methylation values

value: AML


title: p110αδ DKO LMPP (KG2160-MTA1.23)

city: Bronx

first: Shayda

last: Hemmati

address: 1300 Morris Park

institute: Albert Einstein College of Medicine

description: RMA expression value derived from Expression Console software

hyb_protocol: RNA was hybridized to the Gene Chip ® Mouse Transcriptome Pico Assay 1.0 using the GeneChip™ Hybridization, Wash, and Stain Kit

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

data_processing: Raw data were processed with expression console (Affymetrix) for probe set summarization and initial data quality examination. Data analysis and statistical evaluations were performed with Affymatrix Transcriptome analysis console (TAC) with 2 fold change and P value<0.05

organism: Mus musculus

source_name: p110αδ DKO LMPP

label_protocol: Standard Affymetrix protocol

extract_protocol:
RNA isolation was performed using the (ARCTURUS PicoPure RNA Isolation Kit (Life Technologies, Invitrogen) according to the manufacturer’s protocol
[quantification protocol] RNA quantification was performed using the RNA Quantification Kit for SYBR Green I and ROX™ Passive Reference Dye (Thermo Fisher)

value: male

value: LMPP

tag: genotype

value: p110alphadelta DKO


title: RA_IFX treated6__CD8-Tcm cells

value: blood

value: RA IFX treatment


title: Fig5A_24709_t20_IP


title: p110αδ DKO HSC (KG2160-MTA1.22)

source_name: p110αδ DKO HSC

value: HSC


title: AML_AP methylation values

value: F


title: AML_AO methylation values

value: bone marrow

value: M


title: Fig5A_24709_t0_WCE


title: p110δ-/- LMPP (KG2160-MTA1.21)

source_name: p110δ-/- LMPP


title: p110δ-/- HSC (KG2160-MTA1.20)


title: RA_IFX treated6__CD4-Tem cells


title: RA_IFX treated6__CD4-Tn cells

source_name: Tn CD4 cell

value: Tn CD4 cell


title: AML_AN methylation values


title: p110α-/- LMPP (KG2160-MTA1.19)

source_name: p110α-/- LMPP


title: p110α-/- HSC (KG2160-MTA1.18)


title: RA_IFX treated6__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell


title: Fig5A_24709_t0_IP


title: Fig4B_26994_t20_WCE

value: none (input)

value: Arrested in late G1 (Gal-sic1)


title: RA_IFX treated5__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell


title: AML_AM methylation values


title: AML_AL methylation values


title: RA_IFX treated5__CD8-Temra cells

source_name: Temra CD8 cell

value: Temra CD8 cell


title: p110δ-/- LMPP (KG2160-MTA1.17)

value: female


title: p110δ-/- HSC (KG2160-MTA1.16)


title: RA_IFX treated5__CD8-Tem cells

source_name: Tem CD8 cell

value: Tem CD8 cell


title: Fig4B_26994_t0_WCE


title: p110αδ DKO LMPP (KG2160-MTA1.15)


title: AML_AJ methylation values

value: AML


title: AML_AI methylation values


title: RA_IFX treated5__CD4-Tn cells


title: RA_IFX treated5__CD4-Tem cells

source_name: Tem CD4 cell

value: Tem CD4 cell


title: AML_AH methylation values


title: RA_MTX treated1__CD8-Tcm cells

source_name: Tcm CD8 cell

value: Tcm CD8 cell

value: RA MTX treatment


title: p110αδ DKO HSC (KG2160-MTA1.14)

value: p110alphadelta DKO


title: Fig4B_26993_t20_WCE


title: Fig4B_26994_t20_IP

value: anti-PK antibody (Bio-Rad)


title: WT HSC (KG2160-MTA1.13)

source_name: WT HSC

value: male

value: HSC

value: WT


title: Fig4B_26993_t0_WCE


title: Fig4B_26993_t20_IP


title: AML_AG methylation values

source_name: AML bone marrow

value: bone marrow

value: F


title: RA_IFX treated5__CD4-Tcm cells

value: blood

value: Tcm CD4 cell

value: RA IFX treatment


title: RA_IFX treated4__CD8-Tn cells

value: Tn CD8 cell


title: AML_AK methylation values

value: M


title: AML_AF methylation values


title: AML_AE methylation values


title: RA_IFX treated5__CD8-Tcm cells


title: WT LMPP (KG2160-MTA1.12)

source_name: WT LMPP

value: LMPP


title: WT HSC (KG2160-MTA1.11)


title: RA_IFX treated4__CD8-Tcm cells


title: Fig4B_26994_t0_IP

source_name: Saccharomyces cerevisiae cells

value: Arrested in late G1 (Gal-sic1)


title: p110α-/- HSC (KG2160-MTA1.9)

value: female


title: p110α-/- LMPP (KG2160-MTA1.10)


title: p110δ-/- LMPP (KG2160-MTA1.8)


title: WT LMPP (KG2160-MTA1.6)


title: p110δ-/- HSC (KG2160-MTA1.7)


title: Fig4A_26766_t20_WCE

value: none (input)


title: AML_AD methylation values

value: AML


title: Fig4A_26766_t20_IP


title: Fig4A_26766_t0_WCE


title: Fig4B_26993_t0_IP


title: RA_IFX treated4__CD4-Tn cells

value: Tn CD4 cell


title: AML_AB methylation values


title: AML_AC methylation values


title: RA_IFX treated4__CD4-Tem cells

value: Tem CD4 cell


title: RA_IFX treated4__CD4-Tcm cells


title: Fig4A_26766_t0_IP

value: anti-PK antibody (Bio-Rad)


title: AML_AA methylation values


title: Fig4A_26765_t20_WCE


title: RA_IFX treated3__CD8-Tn cells


title: RA_IFX treated3__CD8-Temra cells

value: Temra CD8 cell


title: AMPK-KO_FLAGBirA-TET2-S97E_C2C12_clone2_rep2

city: Macau

first: Gang

last: Li

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

description: processed data file: C2C12_AMPK_KO_TET2_WT_S97E_count.txt

data_processing:
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Sequencing reads were trimmed for adaptor sequences using TrimGalore v0.4.5 and mapped to mm10 whole genome using STAR v2.5.3a in basic two pass mode for paired-end reads with parameters: --outReadsUnmapped None, --chimSegmentMin 12, --alignIntronMax 100000, --ChimSegmentReadGapMax parameter 3, --alignSJstitchMismatchNmax 5 -1 5 5.
Gene expression was quantified using featureCount v1.5.3 with GENCODE gene annotation (Release M12).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw gene count of RNA-seq samples.

source_name: C2C12 myoblasts at day 0

growth_protocol: C2C12 cells were cultured at 37 °C in DMEM supplemented with 10% fetal bovine serum (Invitrogen) in an incubator with 5% CO2. For in vitro differentiation, fully confluent C2C12 cells were washed twice with 1 x PBS, then subjected to differentiation in DMEM supplemented with 2% equine donor serum (Hyclone).

extract_protocol:
Cells were harvested at desired time points for total RNA isolation using RNeasy Mini kit (Qiagen).
RNA-seq library was prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina.

value: C2C12 myoblasts at day 0

tag: developmental stage


title: shILF2_3

city: Tianjin

first: Meng

last: Zhao

address: Huan-hu-xi Road He-xi District

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Basecalls performed using Hiseq.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

source_name: Lung adenocarcinoma cell line

growth_protocol: The celle were cultured in 1640 medium. When the cell density reaches 70%-80%, the cells were lysed

extract_protocol: RNA libraries were prepared for sequencing using  oligo -dT beads

treatment_protocol: The expression of ILF2 in cell lines was knockdown by lentivirus.

value: shILF2 A549 cell line


title: Fig4A_26765_t20_IP


title: p110α-/- LMPP (KG2160-MTA1.4)

value: male

value: bone marrow


title: Fig4A_26765_t0_WCE


title: AMPK-KO_FLAGBirA-TET2-S97E_C2C12_clone2_rep1


title: Fig4A_26765_t0_IP


title: RA_IFX treated3__CD8-Tem cells

value: blood

value: Tem CD8 cell

value: F


title: RA_IFX treated3__CD8-Tcm cells

value: Tcm CD8 cell

value: RA IFX treatment


title: AMPK-KO_FLAGBirA-TET2-S97E_C2C12_clone1_rep2


title: p110αδ DKO HSC (KG2160-MTA1.1)

value: HSC

value: p110alphadelta DKO


title: Fig3C_26415_t20_WCE

value: none (input)

value: Arrested in late G1 (Gal-sic1)


title: AMPK-KO_FLAGBirA-TET2-S97E_C2C12_clone1_rep1


title: scramble2

value: wild A549 cell line


title: scramble1


title: scramble3


title: WT HSC (KG2160-MTA1.5)

value: female

value: WT


title: p110α-/- HSC (KG2160-MTA1.3)


title: p110αδ DKO LMPP (KG2160-MTA1.2)

source_name: p110αδ DKO LMPP

value: LMPP


title: RA_IFX treated3__CD4-Tcm cells

value: Tcm CD4 cell


title: Fig3C_26415_t20_IP

value: anti-PK antibody (Bio-Rad)


title: AMPK-KO_FLAGBirA-TET2-WT_C2C12_clone2_rep1

value: C2C12 myoblasts at day 0


title: Fig3C_26415_t0_WCE


title: shILF2_2

value: shILF2 A549 cell line


title: RA_IFX treated2__CD8-Tn cells

value: blood

value: Tn CD8 cell


title: AMPK-KO_FLAGBirA-TET2-WT_C2C12_clone1_rep2


title: AMPK-KO_FLAGBirA-TET2-WT_C2C12_clone2_rep2


title: shILF2_1


title: RA_IFX treated2__CD8-Temra cells

value: Temra CD8 cell

value: F


title: Fig3C_26414_t20_WCE


title: RA_IFX treated2__CD8-Tcm cells

value: Tcm CD8 cell

value: RA IFX treatment


title: AMPK-KO_FLAGBirA-TET2-WT_C2C12_clone1_rep1


title: AMPK-KO_C2C12_D8_rep2

description: processed data file: C2C12_WT_AMPK_KO_count.txt

source_name: C2C12 myotubes at day 8

value: C2C12 myotubes at day 8

value: AMPK-/-


title: BKS_Control_1

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

data_processing:
To process RNAseq libraries, adaptor sequences were trimmed using Cutadapt version 1.13, requiring a length greater than 20 nt after trimming, and quality-filtered by requiring all bases to have a minimum score of 20 (-m 20 -q 20). Only reads that passed the quality or length threshold on both strands were considered for mapping. Reads were mapped with the spliced-read mapper GSNAP (version 2016-08-10) using default parameters. Reads were aligned against the NCBIM37 (mm9) genome build release 67 downloaded from Ensemble. Reads mapping to the genes of interest were counted using HTseq (v.0.7.1) in the union mode. Differential expression analysis was performed in R using DESeq2 (v.1.16.0) with the default parameters, including the Cook’s distance treatment to remove outliers.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file containing the raw reads count matrix

source_name: BKS_Control_whole islets

extract_protocol:
For islets RNAseq: islets were isolated and RNA was extracted using Trizol reagent.
Sequencing libraries were prepared from 10-25 ng of total RNA using the SMARTer Stranded RNAseq Kit (Clonetech)

tag: strain background

tag: genotype/variation

value: control

value: 4 weeks old

value: whole islets


title: BKS_Db_1

source_name: BKS_Db_whole islets

value: Db


title: BKS_Control_2


title: Fig3C_26414_t0_WCE

tag: sac_cer strain

tag: can_gla strain

value: none (input)

value: Arrested in late G1 (Gal-sic1)


title: Fig3C_26414_t20_IP

tag: antibody

value: anti-PK antibody (Bio-Rad)

tag: timepoint


title: Fig3C_26415_t0_IP


title: AMPK-KO_C2C12_D8_rep1

tag: tissue

tag: cell type


title: RC_TSC1_KO_2

source_name: RC_TSC1_KO_whole islets

value: TSC1 KO

tag: age

value: 8 weeks old


title: Fig3C_26414_t0_IP


title: RA_IFX treated2__CD4-Tcm cells

source_name: Tcm CD4 cell

value: blood

value: Tcm CD4 cell

tag: disease status

tag: gender


title: WT_C2C12_D8_rep1

value: WT


title: AMPK-KO_C2C12_D0_rep2

value: C2C12 myoblasts at day 0


title: RA_IFX treated10__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell

value: F


title: RA_IFX treated2__CD4-Tn cells

source_name: Tn CD4 cell

value: Tn CD4 cell

value: RA IFX treatment


title: RA_IFX treated2__CD4-Tem cells

value: Tem CD4 cell


title: AMPK-KO_C2C12_D0_rep1

value: AMPK-/-


title: Fig3A_27570_t0_IP


title: Adult_2

source_name: adult_pancreatic β-cells

value: wild type

value: pancreatic β-cells


title: Fig3A_27570_t30_WCE

value: none (input)


title: WT_C2C12_D8_rep2

value: C2C12 myotubes at day 8


title: Adult_1


title: RC_Control_2

source_name: RC_Control_whole islets

value: control

value: whole islets


title: RC_TSC1_KO_1

value: TSC1 KO

value: 8 weeks old


title: RA_IFX treated10__CD8-Tcm cells

source_name: Tcm CD8 cell

value: blood

value: Tcm CD8 cell


title: Fig3A_27570_t30_IP

value: anti-PK antibody (Bio-Rad)

value: Arrested in late G1 (Gal-sic1)


title: RC_Control_1


title: Fig3A_27570_t0_WCE


title: INPUT_AMPK_KO_C2C12_D8_clone1

data_processing:
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Sequencing reads were trimmed for adaptor sequences using TrimGalore v0.4.5 and mapped to mm10 whole genome using Bowtie2 v2.3.4.1 with default parameters.
Duplicated reads were removed using Picard v2.18.5 - MarkDuplicates, keeping reads with mapQ>10 that are not within the ENCODE DAC blacklist regions.
BigWig tracks were generated using Deeptools v3.0.2 with RPKM (reads per kilobase per million) normalisation.
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig tracks include RPKM read coverage in 50bp bins for each ChIP-seq sample.

extract_protocol:
Cells were harvested at desired time points for DNA isolation by phenol-chloroform extraction. Methylated DNA immunoprecipitation was carried out with Abcam MEDIP kit (ab117133). The DNA was released by treatment with Proteinase K and further purified for the library DNA preparation.
MeDIP-seq library was prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina according to manufacturer's instructions (NEB#E7645).


title: Neonatal_2

source_name: neonatal_pancreatic β-cells


title: Fig3A_27569_t0_WCE


title: RA_IFX treated10__CD8-Temra cells

source_name: Temra CD8 cell

value: Temra CD8 cell

value: F


title: Adult_3


title: Fig3A_27569_t30_WCE


title: WT_C2C12_D0_rep2

value: C2C12 myoblasts at day 0

value: WT


title: WT_C2C12_D0_rep1


title: Fig2F_26831_t60_WCE

value: Arrested in G2 (Nocodazole)


title: Fig3A_27569_t30_IP


title: RA_IFX treated10__CD4-Tn cells

value: Tn CD4 cell

value: RA IFX treatment


title: INPUT_AMPK_KO_C2C12_D0_clone1

value: AMPK-/-


title: Neonatal_3

value: wild type

value: pancreatic β-cells


title: RA_IFX treated10__CD4-Tem cells

source_name: Tem CD4 cell

value: Tem CD4 cell


title: Fig3A_27569_t0_IP

source_name: Saccharomyces cerevisiae cells


title: Fig2F_26831_t0_WCE

value: none (input)


title: RA_IFX treated10__CD4-Tcm cells

value: Tcm CD4 cell


title: Neonatal_1


title: RA_IFX treated10__CD8-Tem cells

source_name: Tem CD8 cell

value: blood

value: Tem CD8 cell


title: RA_IFX treated1__CD8-Tem cells


title: RA_IFX treated1__CD8-Tn cells

value: Tn CD8 cell


title: INPUT_AMPK_KO_C2C12_D0_clone2

source_name: C2C12 myoblasts at day 0


title: Fig2F_26831_t0_IP

value: anti-PK antibody (Bio-Rad)


title: pbs_neut1

first: Dylan

last: Sheerin

address: Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital

department: Paediatrics

data_processing:
RNA from whole blood was sequenced (150 bp, paired end) using a NovaSeq instrument. Indexed libraries from single cells were pooled in equimolar ratios and sequenced on the Illumina HiSeq 4000 system with a customized paired end (28,8,98 bp) format according to the recommendation by 10X Genomics. [I1 = 8-base MPX index, R1 = Unique molecular identifier, R2 = insert/transcript sequence]
Raw fastq files from whole blood and single cell RNA-seq were analysed for sequence quality using fastqc software and trimmed where necessary using Trimmomatic.
Reads were aligned to the Mus musculus reference genome (GRCm38) and genes were quantified using STAR, with the --quantMode GeneCounts function for the whole blood data. Raw fastq files from the single cell RNA-seq data were aligned, filtered, barcode and UMI counted using the cellranger count function of the Cell Ranger (10x Genomics) pipeline.
Resultant count matrices from the whole blood data were filtered to include only genes with counts per million of greater than 1 million in 6 or more samples (smallest group size). Filtered count matrices were normalised using the RLE method and then analysed for differential gene expression using the limma/voom pipeline.
Single cell data were analysed using the Seurat pipeline, creating objects for each experimental condition to include features detected in at least 3 cells and then filtering the resultant object to keep only cells with fewer than 2% mitochondrial transcripts. An integrated, canonical correlation analysis was then performed to compare each group for neutrophil cluster-specific responses to immunisation.
Genome_build: GRCm38, release 95
Supplementary_files_format_and_content: Tab-delimited files (.tab) were generated for the whole blood RNA-seq data using STAR –quantMode GeneCounts and each value represent the number of reads incident to a gene in a given sample
Supplementary_files_format_and_content: Tab-separated variable (.tsv) files corresponding to sample barcodes and genes were generated for each sample from the single cell data using the Cell Ranger (10x Genomics) pipeline. 10x counts are stored in the matrix (.mtx) files for each sample. For further processing, a folder should be created for each sample and the sample prefix removed to generate a barcodes.tsv, genes.tsv, and matrix.mtx file for each sample.

source_name: Neutrophils

extract_protocol:
RNA was extracted from mouse whole blood samples using a Mouse RiboPure(TM)-Blood RNA Isolation Kit (Life Technologies) and depleted for glibin mRNA using a GLOBINclear(TM) mouse/rat Kit (Life Technologies).
Polyadenylated transcripts from RNA extracted from whole blood were oligo (dT) bead-selected, reverse transcribed, amplified and labelled with an Illumina TotalPrep(TM)-96 RNA Amplification Kit (Life Technologies). RNA transcripts from single cells were reverse-transcribed within droplets to generate barcoded full-length cDNA. cDNA molecules from each sample were recovered and amplified.
Sample fragments from whole blood RNA samples were 150 bp size-selected and multiplexed. The size profiles of the amplified cDNA  and sequencing from single cells libraries were assessed by an Agilent 2200 TapeStation using High Sensitivity D5000 and D1000 ScreenTapes, respectively (Agilent Technologies).

treatment_protocol: Groups of 6 female C57BL/6 mice (6-8 weeks old) were immunised intramuscularly with 1/15 of the human dose of one of the listed vaccines. Mice were given a second dose of vaccine 3 weeks later and cardiac bled to obtain whole blood 24h ours after this second dose. For the single cell analysis, neutrophils were sorted from red blood cell-lysed blood samples using a FACSAria(TM) and gating on Ly6C-Cd11b+Ly6G+ live cells. Droplet-based single-cell partitioning and scRNA-seq libraries were generated using the Chromium Single-Cell 3’ Reagent v3 Kits (10X Genomics) as per the manufacturer’s protocol.

tag: strain

value: Female

tag: vaccine/antigen

value: PBS control


title: rout_neut1

tag: Sex

value: Routine only


title: RA_IFX treated1__CD4-Tem cells

value: F


title: conc_neut1

value: 4CMenB + routine


title: 5mC_AMPK_KO_C2C12_D8_clone2

source_name: C2C12 myotubes at day 8

value: C2C12 myotubes at day 8


title: 5mC_AMPK_KO_C2C12_D8_clone1


title: RA_IFX treated1__CD8-Temra cells

value: Temra CD8 cell

value: RA IFX treatment


title: INPUT_AMPK_KO_C2C12_D8_clone2

value: AMPK-/-


title: Fig2F_26831_t60_IP

value: Arrested in G2 (Nocodazole)


title: DDT17C [S277]

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

source_name: dark:dark_time point 17_whole organism

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: Animals were experimentally exposed to either light:dark (LD) or dark:dark (DD) conditions for 1 month, then sampled every 4 hours for 1 day (24 hours), then in the LD treatment, the light cycle was removed and animals were continually sampled from both LD and DD for 2 more days (44 more hours)

tag: genome

value: Putnam et al. (2007)

tag: light

value: dark cycling timepoint:dark:dark, time point 17, replicate C

value: adult


title: DDT17D [S278]

value: dark cycling timepoint:dark:dark, time point 17, replicate D


title: INPUT_WT_C2C12_D0

value: C2C12 myoblasts at day 0

tag: developmental stage

tag: genotype

value: WT


title: DDT17B [S276]

value: dark cycling timepoint:dark:dark, time point 17, replicate B


title: Fig2F_20891_t0_WCE

value: none (input)


title: INPUT_WT_C2C12_D8


title: RA_IFX treated1__CD8-Tcm cells

value: blood

value: Tcm CD8 cell


title: HC9__CD8-Temra cells

value: healthy

value: F


title: RA_IFX treated1__CD4-Tcm cells

value: Tcm CD4 cell


title: Fig2E_26831_t60_WCE

value: Arrested in late G1 (Gal-sic1)


title: Fig2F_20891_t60_WCE


title: HC9__CD8-Tn cells

value: Tn CD8 cell


title: Fig2F_20891_t60_IP

value: anti-PK antibody (Bio-Rad)


title: 5mC_WT_C2C12_D8

value: C2C12 myotubes at day 8


title: 5mC_AMPK_KO_C2C12_D0_clone2

value: AMPK-/-


title: DDT17A [S275]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 17, replicate A


title: 5mC_AMPK_KO_C2C12_D0_clone1


title: Fig2E_26831_t60_IP


title: Fig2E_26831_t0_WCE


title: Fig2F_20891_t0_IP

value: Arrested in G2 (Nocodazole)


title: LDT17D [S274]

source_name: light:dark_time point 17_whole organism

value: dark cycling timepoint:light:dark, time point 17, replicate D

value: adult


title: LDT17A [S271]

value: dark cycling timepoint:light:dark, time point 17, replicate A


title: HC9__CD8-Tem cells

value: Tem CD8 cell


title: LDT17C [S273]

value: dark cycling timepoint:light:dark, time point 17, replicate C


title: HC9__CD8-Tcm cells

value: blood

value: Tcm CD8 cell


title: LDT17B [S272]

value: dark cycling timepoint:light:dark, time point 17, replicate B


title: Dox24hrB PRO-seq

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: PRO-seq

data_processing:
Library strategy: PRO-seq
Quality control for PROseq: Adapter sequences were trimmed with cutadapt v1.8.2. Nucleotides with poor 3’ base quality (BAPQ < 20) were trimmed and reads of <20 bp were discarded.
Quality control for mRNAseq: First ten bases from all reads were removed, due to their low quality, using FASTX toolkit (v0.0.13).
Genome reconstruction: The VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf) reporting all SNP sites from 36 mouse strains, based on mm10, was downloaded from the Sanger database. SNPsplit tool (v0.3.0) was used to reconstruct the Cast genome from the mm10 reference.
Mapping for PROseq: Ribosomal reads were first removed by alignment to the rRNA reference using bowtie1 (v1.0.0) and allowing 2 mismatches in the seed. Then, non-ribosomal reads were mapped to both parental genomes. Only random best alignments with fewer than two mismatches were kept for downstream analyses.
Mapping for mRNAseq: Reads were then mapped to both parental genomes with TopHat2 software (v2.1.0). Only random best alignments with less than two mismatches were kept for downstream analyses.
Allelic Ratio: Mapping files of both parental genomes were merged for each sample and SAMtools mpileup (v1.1) was then used to extract the base-pair information at each genomic position. Read counts mapping to the paternal and maternal genomes, respectively, were summed up across all SNPs present in the same gene.
Estimation of gene expression levels: RPKM values were calculated using gene count table, generated with Gencode annotation (M9) and HTSeq software (v0.6.1).
Genome_build: mm10

source_name: ES cells

growth_protocol: The female TX1072 cell line is a F1 hybrid ESC line derived from a cross between the  57BL/6 (B6) and CAST/EiJ (Cast) mouse strains that carries a doxycycline responsive promoter in front of the Xist gene on the B6 chromosome and an rtTA insertion in the Rosa26 locus (described in Schulz et al. (Schulz et al., 2014) ). TX1072 cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Chemicon)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901).

extract_protocol:
For PROseq samples: For each timepoint ~1 x 107 nuclei were isolated by washing the cells twice with ice-cold PBS, and once with 15 ml swelling buffer (10 mM Tris-Cl, pH 7.4, 300 mM Sucrose, 3 mM CaCl2, 2 mM MgAc2, 5 mM DTT). Then, 15 ml cell lysis buffer (10 mM Tris-Cl, pH 7.4, 300 mM Sucrose, 3 mM CaCl2, 2 mM MgAc2, 0.5% NP-40, 1 mM PMSF, EDTA-free protease inhibitors (1 tablet for 50 ml buffer; Roche), 5 mM DTT) is added and cells are scraped off the plate into a 50 ml tube and spun at 900 g and 4 °C in a swing bucket centrifuge for 5 minutes. Supernatant is removed and the cell pellet is resuspended in 5 ml cell lysis buffer, transferred to a 7 ml dounce homogenizer and dounced 50x on ice. Dounced cells are moved to 15 ml tube and spun at 1200 g and 4 °C in a swing bucket centrifuge for 5 minutes. Supernatant is removed and the nuclei are counted, snap frozen and stored in glycerol storage buffer (50 mM Tris-Cl, pH 8.3, 40% glycerol, 0.1 mM EDTA, 5 mM MgAc2, 1 mM PMSF, EDTA-free protease inhibitors (1 tablet for 50 ml buffer; Roche), 5 mM DTT).
For PROseq samples: Run-on and library preparation was performed as previously described (Mahat et al., 2016), using the single biotin-CTP nucleotide run-on protocol to prolong run-on and increase sequence length. In short, run-on was performed with 1 x 107 nuclei in 100 ml glycerol storage buffer and 100 ml pre-heated nuclear run-on mix, to get a final concentration in the run-on of 5 mM Tris-HCl, pH 8, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.025 mM biotin-11-CTP, 0.25 mM CTP, 0.125 mM ATP, UTP and GTP, 0.5% sarkosyl and RNase inhibitor. Run-on was done for 5 minutes at 37 °C and stopped by adding 500 ml Trizol LS.
For mRNAseq samples: The 32 libraries were prepared with an input of 1µg of totalRNA, using the TruSeq Stranded mRNA LT Sample Prep kit from Illumina, according to manufacturer's recommendations. Single Index kit was used, and 12 cycles of PCR were set up. Final libraries were quantified with Qubit dsDNA HS Assay Kit, and qualified with LabChip® GX system (PerkinElmer). Then 2 equimolar pools of 16 libraries each were prepared at 10nM. The exact molarity of the pools were assess by qPCR using the KAPA Library Quantification Kit Illumina on CFX96 system (Biorad).
For PROseq samples: Libraries were sequenced on the HiSeq 2000 Illumina sequencer (100bp, single-end). For each library at least 50 Mio reads were generated.
For mRNAseq samples: Each pool was sequenced on 1 flowcell of HiSeq 2500 system in PE100, in order to target ~100M cluster per sample.

treatment_protocol: Cells were seeded at a density of 105 cells/cm2 coated with gelatin two days before the experiment. Xist was induced by supplementing the medium with 1 μg/ml Doxycycline. For PRO-seq samples were collected before doxycycline treatment (0h) and at time points 0.5, 1, 2, 4, 8, 12 and 24h after treatment. Samples without doxycycline and 24 h doxycycline were collected in duplicate. For mRNA-Seq on undifferentiated TX1072 cells, samples were collected before doxycycline treatment and at time points 2, 4, 8, 12 and 24h after treatment. Also for mRNA-seq samples without doxycycline and 24 h doxycycline were collected in duplicate. For mRNA-Seq on differentiating TX1072 cells samples were collected at time points 0, 8, 16, 24 and 48h.

tag: doxycycline treatment (h)

value: Undifferenciated ES cells


title: DDT16D [S270]

source_name: dark:dark_time point 16_whole organism

value: dark cycling timepoint:dark:dark, time point 16, replicate D


title: HC9__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell

value: healthy

value: F


title: DDT16C [S269]

value: dark cycling timepoint:dark:dark, time point 16, replicate C


title: Fig2E_20891_t60_IP

tag: sac_cer strain

value: anti-PK antibody (Bio-Rad)

value: Arrested in late G1 (Gal-sic1)


title: 5mC_WT_C2C12_D0

value: C2C12 myoblasts at day 0

value: WT


title: HC8__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell


title: Dox4hr PRO-seq

description: PRO-seq


title: HC9__CD4-Tem cells

value: Tem CD4 cell


title: Fig2E_20891_t60_WCE

tag: can_gla strain

value: none (input)


title: Dox12hr PRO-seq

description: PRO-seq


title: DDT16B [S268]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 16, replicate B

value: adult


title: Fig2E_26831_t0_IP

tag: antibody


title: Dox8hr PRO-seq

description: PRO-seq


title: Dox24hrA PRO-seq

description: PRO-seq


title: Fig2E_20891_t0_WCE

tag: timepoint


title: HC8__CD8-Temra cells

tag: tissue

value: blood

value: Temra CD8 cell


title: HC9__CD4-Tn cells

source_name: Tn CD4 cell

tag: cell type

value: Tn CD4 cell


title: DDT16A [S267]

value: dark cycling timepoint:dark:dark, time point 16, replicate A

tag: age


title: Dox2hr PRO-seq

description: PRO-seq

value: Undifferenciated ES cells


title: BKS_Db_2

source_name: BKS_Db_whole islets

tag: strain background

tag: genotype/variation

value: Db

value: 4 weeks old

value: whole islets


title: RA_IFX treated3__CD4-Tn cells

tag: disease status

value: RA IFX treatment

tag: gender

value: F


title: Fig2E_20891_t0_IP

value: anti-PK antibody (Bio-Rad)

value: Arrested in late G1 (Gal-sic1)


title: HC8__CD8-Tem cells

value: Tem CD8 cell

value: healthy


title: Dox1hr PRO-seq

description: PRO-seq

tag: strain


title: LDT16D [S266]

source_name: light:dark_time point 16_whole organism

tag: genome

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 16, replicate D


title: Fig2B_22296_t20_WCE

value: none (input)

value: Arrested in G2 (Nocodazole)


title: Dox30min PRO-seq

description: PRO-seq


title: NoDoxB PRO-seq

description: PRO-seq


title: Fig2B_22296_t20_IP


title: HC8__CD4-Tn cells

value: blood


title: HC8__CD4-Tem cells

value: Tem CD4 cell


title: LDT16A [S263]

tag: light

value: dark cycling timepoint:light:dark, time point 16, replicate A

value: adult


title: NoDoxA PRO-seq

description: PRO-seq

value: Undifferenciated ES cells


title: LDT16B [S264]

value: dark cycling timepoint:light:dark, time point 16, replicate B


title: RA_IFX treated3__CD4-Tem cells


title: Fig2B_22296_t0_WCE


title: DDT15D [S262]

source_name: dark:dark_time point 15_whole organism

value: dark cycling timepoint:dark:dark, time point 15, replicate D


title: HC8__CD4-Tcm cells

value: Tcm CD4 cell


title: Fig2B_22296_t0_IP


title: Fig2B_22294_t20_WCE


title: DDT15C [S261]

value: dark cycling timepoint:dark:dark, time point 15, replicate C


title: HC7__CD8-Tn cells

value: Tn CD8 cell

value: F


title: Fig2B_22294_t20_IP

value: anti-PK antibody (Bio-Rad)


title: TIC_shH19_miRNA

city: New Orleans

first: Jinqiang

last: Zhang

address: 1430 Tulane Ave

department: Pathology

institute: Tulane University

data_processing:
For mRNA, Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
For miRNA, Sequence reads were trimmed to remove possible adapter sequences at the 3’ end. After trimming, sequence reads with 15 to 31 nucleotides were retained for subsequent analysis.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: TICs

extract_protocol:
RNA from TICs was harvested using Qiagen RNeasy Mini Kit with standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: H19 knockdown

value: Tumor Initiating hepatoCytes (TICs)


title: HC8__CD8-Tcm cells

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.0.4.0).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.0.4.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: Tcm CD8 cell

extract_protocol:
Total RNA from were extracted using RNeasy Micro kit (Qiagen).
0.2 or 1 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit. Then cDNA is amplified using Ion AmpliSeq™ technology. After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 75 pM and pooled equally, with eighteen individual samples per pool.

value: Tcm CD8 cell

value: healthy


title: TIC_shH19_mRNA


title: TIC_shcont_miRNA

value: control


title: DDT15B [S260]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 15, replicate B


title: HC7__CD8-Temra cells

source_name: Temra CD8 cell

value: blood

value: Temra CD8 cell


title: HC7__CD8-Tem cells

source_name: Tem CD8 cell

value: Tem CD8 cell


title: Fig2B_22294_t0_WCE

source_name: Saccharomyces cerevisiae cells

value: none (input)

value: Arrested in G2 (Nocodazole)


title: LDT16C [S265]

value: dark cycling timepoint:light:dark, time point 16, replicate C

value: adult


title: DDT15A [S259]

value: dark cycling timepoint:dark:dark, time point 15, replicate A


title: HC7__CD8-Tcm cells

value: F


title: 606T

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

institute: Institut Pasteur

data_processing:
Basecalling was performed with Illumina RTA 1.18.64. Bcl conversions into Fastq were performed using bcl2fastq version 1.8.3.
Reads were mapped to mm10 genome with STAR version 2.4.0g1 using Ensembl annotation (GRCm38, release 78)
Duplicate reads were removed using the function MarkDuplicates from Picard tools and a filtering for uniquely mapped reads was performed.
We quantified read counts for all genes annotated in Ensembl release 78 with HTSeqcount version 0.6.1
Differential gene expression analysis was performed with the Bioconductor package DESeq2 version 1.6.3 and SARTools version 1.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including differential expression results from DESeq2

molecule: polyA RNA

source_name: Thymic lymphoma

extract_protocol:
RNA was prepared from single-cell suspensions of mouse tumor thymus using the RNeasy Mini Kit (Qiagen).
Libraries were generated according to the TruSeq Stranded mRNA Library Preparation kit protocol (Illumina)

value: mixed background C57BL/6 and 129S6/SvEv


title: Fig2B_22294_t0_IP

value: anti-PK antibody (Bio-Rad)


title: LDT15D [S258]

source_name: light:dark_time point 15_whole organism

value: dark cycling timepoint:light:dark, time point 15, replicate D


title: HC7__CD4-Tn cells

first: Masaru

last: Takeshita

address: 35 shinanomachi

value: Tn CD4 cell


title: Fig2A_22296_t20_WCE

value: Arrested in late G1 (Gal-sic1)


title: 378T


title: 264T


title: Fig2A_22296_t20_IP


title: LDT15B [S256]

value: dark cycling timepoint:light:dark, time point 15, replicate B


title: Fig2A_22296_t0_WCE


title: 261T


title: HC7__CD4-Tcm cells

value: Tcm CD4 cell

value: healthy


title: LDT15A [S255]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 15, replicate A


title: Fig2A_22296_t0_IP


title: HC6__CD8-Tn cells

value: blood

value: Tn CD8 cell


title: DDT14D [S254]

source_name: dark:dark_time point 14_whole organism

value: dark cycling timepoint:dark:dark, time point 14, replicate D


title: LDT15C [S257]

value: dark cycling timepoint:light:dark, time point 15, replicate C


title: 259T


title: TIC_shcont_mRNA

value: control

value: Tumor Initiating hepatoCytes (TICs)


title: Fig2A_22294_t20_WCE

value: none (input)


title: HC6__CD8-Temra cells

value: Temra CD8 cell

value: F


title: Fig2A_22294_t20_IP

value: anti-PK antibody (Bio-Rad)


title: ThymusWT3

source_name: Thymus

value: wild type


title: HC6__CD8-Tcm cells

value: Tcm CD8 cell


title: Fig2A_22294_t0_WCE

value: Arrested in late G1 (Gal-sic1)


title: DDT14B [S252]

value: dark cycling timepoint:dark:dark, time point 14, replicate B

value: adult


title: ThymusWT1


title: DDT14C [S253]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 14, replicate C


title: ThymusWT2


title: Fig2A_22294_t0_IP


title: LDT14D [S250]

source_name: light:dark_time point 14_whole organism

value: dark cycling timepoint:light:dark, time point 14, replicate D


title: Fig1F_25316t20_WCE


title: HC6__CD4-Tem cells

source_name: Tem CD4 cell

value: blood

value: Tem CD4 cell

value: healthy


title: HC7__CD4-Tem cells


title: LDT14C [S249]

value: dark cycling timepoint:light:dark, time point 14, replicate C


title: HC6__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell


title: Fig1F_25316t20_IP


title: HC5__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell


title: Fig1F_25313t20_WCE

value: none (input)


title: LDT14B [S248]

value: dark cycling timepoint:light:dark, time point 14, replicate B


title: DDT13D [S246]

source_name: dark:dark_time point 13_whole organism

value: dark cycling timepoint:dark:dark, time point 13, replicate D


title: DDT14A [S251]

value: dark cycling timepoint:dark:dark, time point 14, replicate A


title: Fig1F_25316t0_WCE


title: LDT14A [S247]

value: dark cycling timepoint:light:dark, time point 14, replicate A


title: Fig1F_25313t20_IP

value: anti-PK antibody (Bio-Rad)

value: Arrested in late G1 (Gal-sic1)


title: HC5__CD8-Temra cells

value: Temra CD8 cell

value: F


title: HC6__CD8-Tem cells

value: Tem CD8 cell


title: HC5__CD8-Tcm cells

value: Tcm CD8 cell


title: DDT13C [S245]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 13, replicate C

value: adult


title: Fig1F_25316t0_IP


title: Fig1F_25313t0_WCE


title: HC5__CD4-Tn cells

source_name: Tn CD4 cell

value: blood

value: Tn CD4 cell

value: healthy


title: DDT13A [S243]

value: dark cycling timepoint:dark:dark, time point 13, replicate A


title: HC6__CD4-Tn cells


title: nonTEC ShCxD7 rep1

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The microarray data was processed using limma.  Probes with a detection P-value < 0.95 were removed, then limma function neqc() was used to perform normexp background correction, and quantile normalisation

source_name: nonTEC ShCxD7

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit for Illumina arrays

extract_protocol: Thymic epithlieal cells (TECs) or non-TECs stromal cells were FACS sorted. RNA was purified from TEC (CD45-EpCAM+) and non-TEC (CD45-EpCAM-) samples using a Qiagen RNEasy Kits and total RNA was quality ascertained using the Agilent Bioanalyser 2100 and NanoChip protocol

treatment_protocol: Animals were surgically castrated, or sham-castrated, or no treatment controls

value: male

value: 9-12 months old

tag: time point

value: day 7 post sham-castration

value: thymus

value: non TEC stromal cells


title: nonTEC ShCxD7 rep2


title: Fig1F_25313t0_IP

value: anti-PK antibody (Bio-Rad)

value: Arrested in late G1 (Gal-sic1)


title: nonTEC CxD7 rep1

source_name: nonTEC CxD7

value: day 7 post castration


title: nonTEC ShCxD4 rep3

source_name: nonTEC ShCxD4

value: day 4 post sham-castration


title: nonTEC CxD7 rep2


title: HC5__CD4-Tem cells

city: sinjuku-ku

institute: Keio University

value: Tem CD4 cell

value: F


title: DDT13B [S244]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 13, replicate B


title: HC5__CD8-Tem cells

value: blood

value: Tem CD8 cell


title: HC5__CD4-Tcm cells

value: Tcm CD4 cell

value: healthy


title: HC4__CD8-Tn cells

value: Tn CD8 cell


title: HC4__CD8-Temra cells

value: Temra CD8 cell


title: LDT13C [S241]

source_name: light:dark_time point 13_whole organism

value: dark cycling timepoint:light:dark, time point 13, replicate C

value: adult


title: LDT13D [S242]

value: dark cycling timepoint:light:dark, time point 13, replicate D


title: LDT13B [S240]

value: dark cycling timepoint:light:dark, time point 13, replicate B


title: HC4__CD8-Tem cells


title: LDT13A [S239]

value: dark cycling timepoint:light:dark, time point 13, replicate A


title: preosteoclast

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

institute: Third Military Medical University

data_processing:
FastQC software was used for reads quality evaluation.
Fastp software was used for reads filtering to get clean reads.
Hisat2 software was used for spliced mapping with mouse genome GRCm38.
Circos software was used for chromosomal mapping.
Stringtie software was used for counting of fragments and trimmed mean of M values (TMM) was used for normalization.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited xls files include FPKM values for each Sample concerning mRNA, lncRNA and circRNA

source_name: Bone marrow

growth_protocol: BMMs were used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more.

extract_protocol:
Femurs and tibia were dissected from mice and flushed using complete medium to acquire whole bone marrow. The whole cells were cultured using alpha-MEM complete media for 24 h and the floating cells were collected for further treatment of M-CSF (50ng/mL) for 72 h to generate BMMs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of alendronate (500 μM for 12 h) to cell culture medium to induce the generation of apoptotic bodies.

value: Bone marrow

value: preosteoclast

value: post natal week 11


title: mature osteoclasts

value: mature osteoclast


title: bone marrow macrophages

value: bone marrow macrophages


title: DDT12C [S237]

source_name: dark:dark_time point 12_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 12, replicate C


title: HC4__CD8-Tcm cells

source_name: Tcm CD8 cell

value: blood

value: Tcm CD8 cell

value: F


title: HC4__CD4-Tn cells

value: Tn CD4 cell

value: healthy


title: nonTEC ShCxD4 rep2

value: male

value: 9-12 months old

value: day 4 post sham-castration

value: thymus

value: non TEC stromal cells


title: nonTEC ShCxD4 rep1


title: HC4__CD4-Tem cells

value: Tem CD4 cell


title: bex6

source_name: Whole blood

tag: Sex

value: Female

tag: vaccine/antigen

value: 4CMenB only


title: bex5


title: nonTEC CxD7 rep3

value: day 7 post castration


title: DDT12B [S236]

value: dark cycling timepoint:dark:dark, time point 12, replicate B

value: adult


title: nonTEC CxD4 rep2

source_name: nonTEC CxD4

value: day 4 post castration


title: nonTEC Normal Young rep3

source_name: nonTEC Normal Young

value: young (5-6wk old)


title: DDT12A [S235]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 12, replicate A


title: HC3__CD8-Tn cells

value: blood

value: Tn CD8 cell

value: F


title: nonTEC CxD4 rep3

value: male

value: 9-12 months old


title: nonTEC Normal Young rep1

value: thymus


title: bex4


title: HC4__CD4-Tcm cells

value: Tcm CD4 cell

value: healthy


title: bex3

value: Female


title: bex1

value: 4CMenB only


title: HC3__CD8-Tcm cells

value: Tcm CD8 cell


title: DDT12D [S238]

value: dark cycling timepoint:dark:dark, time point 12, replicate D


title: contr5

value: PBS control


title: DDT11D [S230]

source_name: dark:dark_time point 11_whole organism

value: dark cycling timepoint:dark:dark, time point 11, replicate D

value: adult


title: LDT12C [S233]

source_name: light:dark_time point 12_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 12, replicate C


title: DDT11C [S229]

value: dark cycling timepoint:dark:dark, time point 11, replicate C


title: bex2


title: HC3__CD4-Tn cells

value: blood

value: Tn CD4 cell


title: HC3__CD8-Temra cells

source_name: Temra CD8 cell

value: Temra CD8 cell

value: F


title: HC3__CD4-Tem cells

source_name: Tem CD4 cell

value: Tem CD4 cell


title: LDT12B [S232]

value: dark cycling timepoint:light:dark, time point 12, replicate B


title: LDT12A [S231]

value: dark cycling timepoint:light:dark, time point 12, replicate A


title: contr4

value: Female


title: nonTEC Normal Young rep2

value: male

value: young (5-6wk old)

value: thymus

value: non TEC stromal cells


title: DDT11B [S228]

value: dark cycling timepoint:dark:dark, time point 11, replicate B


title: nonTEC CxD4 rep1

value: 9-12 months old

value: day 4 post castration


title: HC3__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell

value: healthy


title: LDT12D [S234]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 12, replicate D

value: adult


title: DDT11A [S227]

value: dark cycling timepoint:dark:dark, time point 11, replicate A


title: contr6

value: PBS control


title: contr3


title: HC3__CD8-Tem cells

source_name: Tem CD8 cell

value: blood

value: Tem CD8 cell

value: F


title: LDT11D [S226]

source_name: light:dark_time point 11_whole organism

value: dark cycling timepoint:light:dark, time point 11, replicate D


title: nonTEC Normal Aged rep1

source_name: nonTEC Normal Aged

value: male

value: middle-aged (9-12mo old)


title: contr2

value: Female


title: contr1


title: LDT11C [S225]

value: dark cycling timepoint:light:dark, time point 11, replicate C


title: nonTEC Normal Aged rep3

value: thymus

value: non TEC stromal cells


title: nonTEC Normal Aged rep2


title: HC2__CD8-Tem cells


title: HC2__CD8-Tn cells

source_name: Tn CD8 cell

value: Tn CD8 cell


title: rout6

value: Routine only


title: rout5


title: HC2__CD8-Tcm cells

value: Tcm CD8 cell

value: healthy


title: LDT11B [S224]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 11, replicate B

value: adult


title: HC2__CD4-Tn cells

source_name: Tn CD4 cell

value: blood

value: Tn CD4 cell


title: TEC ShCxD20 rep3

source_name: TEC ShCxD20

value: 9-12 months old

value: day 20 post sham castration

value: thymic epithelial cell (TEC)


title: TEC CxD20 rep3

source_name: TEC CxD20

value: male

value: day 20 post castration


title: TEC ShCxD20 rep1


title: TEC ShCxD20 rep2


title: TEC CxD20 rep2


title: LDT11A [S223]

value: dark cycling timepoint:light:dark, time point 11, replicate A


title: rout4

value: Female


title: DDT10D [S222]

source_name: dark:dark_time point 10_whole organism

value: dark cycling timepoint:dark:dark, time point 10, replicate D


title: DDT10C [S221]

value: dark cycling timepoint:dark:dark, time point 10, replicate C


title: HC2__CD4-Tcm cells

value: Tcm CD4 cell

value: F


title: DDT10B [S220]

value: dark cycling timepoint:dark:dark, time point 10, replicate B


title: TEC CxD4 rep3

source_name: TEC CxD4

value: day 4 post castration

value: thymus


title: DDT10A [S219]

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 10, replicate A

value: adult


title: TEC Normal Aged rep3

source_name: TEC Normal Aged

value: 9-12 months old


title: HC10__CD8-Temra cells

value: blood

value: Temra CD8 cell

value: healthy

value: M


title: TEC CxD20 rep1

value: male

value: day 20 post castration

value: thymic epithelial cell (TEC)


title: rout2

source_name: Whole blood

value: Female

value: Routine only


title: rout3


title: HC10__CD8-Tem cells

value: Tem CD8 cell


title: HC2__CD4-Tem cells

value: Tem CD4 cell

value: F


title: LDT10D [S218]

source_name: light:dark_time point 10_whole organism

value: dark cycling timepoint:light:dark, time point 10, replicate D


title: conc5

value: 4CMenB + routine


title: HC10__CD8-Tcm cells

source_name: Tcm CD8 cell

value: Tcm CD8 cell


title: LDT10C [S217]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 10, replicate C

value: adult


title: conc4


title: TEC CxD4 rep2

value: 9-12 months old

value: day 4 post castration

value: thymus


title: HC10__CD8-Tn cells

value: blood

value: Tn CD8 cell

value: healthy

value: M


title: rout1

value: Female

value: Routine only


title: LDT10B [S216]

value: dark cycling timepoint:light:dark, time point 10, replicate B


title: conc6


title: conc3


title: conc2


title: LDT10A [S215]

value: dark cycling timepoint:light:dark, time point 10, replicate A


title: conc1


title: TEC ShCxD7 rep3

source_name: TEC ShCxD7

value: male

value: day 7 post sham-castration

value: thymic epithelial cell (TEC)


title: HC1__CD8-Temra cells

source_name: Temra CD8 cell

value: Temra CD8 cell


title: HC1__CD8-Tn cells


title: HC10__CD4-Tn cells

value: Tn CD4 cell


title: HC10__CD4-Tem cells

source_name: Tem CD4 cell

value: Tem CD4 cell


title: HC10__CD4-Tcm cells

source_name: Tcm CD4 cell

value: Tcm CD4 cell


title: DDT9C [S213]

source_name: dark:dark_time point 9_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:dark:dark, time point 9, replicate C

value: adult


title: RNA-Seq_CD8SP-EomesTG_S2

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

description:
Truseq kit
RNA-Seq_CD8SP_EomesTGvsWT_CP20M.csv
RNA-Seq_CD8SP_EomesTGvsWT_DifferentialAnalysisResults.xlsx

data_processing:
reads were filtered using FastX 0.0.13 and ShortRead 1.16.3, polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type) were removed
reads were aligned to the reference genome mm10 using Tophat v2.0.13 with the following parameters: --library-type fr-firststrand --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3
reads from the alignment that are non-primary mappings or have a mapping quality ≤20 were removed
read counts were estimated using featureCounts v1.4.6 with the following parameters: -Q 0 -s 2 -t exon -g gene_id and genes that have less than 1 counts-per-million were removed
raw read  counts were normalised with the EDASeq package and FPKM values were obtained
differential expression analysis was performed with edgeR 3.4.0 package by applying a corrected p value FDR<0.05 and absolute log2-ratio larger than 1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing raw read counts and FPKM normalized counts (TIM vs Naive) and  tab-delimited text files containing normalized read counts (such as total read count=20M)  for each sample and gene and differential analysis results (EomesTG vs WT)

source_name: Thymus

extract_protocol:
RNA from 106 sorted CD8SP populations was extracted using RNeasy Plus Mini kit according to manufacturer’s instructions
RNA library was prepared using Truseq Ribo zero gold kit for TIM and Naive, and Truseq kit for CD8SP WT and CD8SP EomesTg following manufacturer's instruction.

value: Thymocytes

tag: Stage

value: CD8SP EomesTG

tag: genotype

value: EomesTg/Tg


title: TEC CxD4 rep1

value: 9-12 months old

value: day 4 post castration

value: thymus


title: TEC ShCxD4 rep3

source_name: TEC ShCxD4

value: day 4 post sham-castration


title: DDT9D [S214]

value: dark cycling timepoint:dark:dark, time point 9, replicate D


title: RNA-Seq_CD8SP-EomesTG_S1


title: DDT9B [S212]

value: dark cycling timepoint:dark:dark, time point 9, replicate B


title: RNA-Seq_CD8SP-EomesTG_S3


title: TEC CxD7 rep2

source_name: TEC CxD7

value: male

value: day 7 post castration

value: thymic epithelial cell (TEC)


title: TEC ShCxD7 rep2

value: day 7 post sham-castration


title: DDT9A [S211]

value: dark cycling timepoint:dark:dark, time point 9, replicate A


title: HC1__CD8-Tem cells

source_name: Tem CD8 cell

value: blood

value: Tem CD8 cell

value: healthy

value: M


title: TEC ShCxD7 rep1


title: HC1__CD8-Tcm cells

value: Tcm CD8 cell


title: RNA-Seq_CD8SP-WT_S3

value: Thymocytes

value: CD8SP WT

value: wild type


title: TEC CxD7 rep3

value: 9-12 months old

value: thymus


title: RNA-Seq_CD8SP-WT_S2


title: HC1__CD4-Tn cells

source_name: Tn CD4 cell

value: Tn CD4 cell


title: LDT9D [S210]

source_name: light:dark_time point 9_whole organism

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 9, replicate D

value: adult


title: MG63-3_E9_treated_rep3: RNA Seq

city: Cleveland Heights

first: Peter

last: Scacheri

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

data_processing:
The FASTX-Toolkit v0.0.13 was used to remove adapter sequences and trim reads with the quality cutoff of 20, excluding any reads shorter than 25bp. ChIP-seq reads were aligned to hg19 with Bowtie 2 v2.0.649, searching for multiple alignments but reporting the one with the best mapping quality score. PCR duplicates were removed using SAMtools 1.2. Peaks were detected with MACS2 2.1.1.20160309 with an input DNA sample as control, scaling the input dataset to match the read depth of the ChIP dataset. MACS2 peaks with a q-value of greater than 0.001 and overlapping ENCODE blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were filtered out. BigWIGs were generated with DeepTools v3.0.1-2-2fa58e8 and normalized to 1x average coverage (RPGC option)
Cutadapt v1.14 was used to trim 3’ adapters, discarding trimmed reads shorter than 20bp. Sickle v1.33 was then used to trim reads with the quality cutoff of 20. RNA-Seq reads were aligned to hg19 assembly plus ERCC RNA Spike-In DNA sequences with STAR v2.5.3a. Cufflinks v2.0.2 was run with genomic bias correction to quantify the levels of transcripts in the hg19 reFLAT annotations file as well as the ERCC transcripts file. Scatter plots of ERCC transcript FPKMs versus their expected concentrations in the spike-in mix were constructed to aid in quality control assessment of the data. The FPKM table was then floored to the background noise level of 0.3. Differential expression analysis between E9-treated and untreated samples was performed by calculating the fold change of mean E9 FPKM over mean DMSO FPKM.
After removing adapter sequences using cutadapt v1.8.1,1 the DNA FASTQ files were aligned to the hg19 reference genome using BWA-mem (v0.7.17-r1188).2,3 The aligned files were then indexed and had PCR duplicates removed using samtools (v0.1.18).4 Each BAM file underwent base quality score recalibration using GATK(v4.0.1.1).5
Refseq hg19 genes underwent the following filtering steps prior to use in downstream analyses for each pair of treated and untreated samples to ensure 1-to-1 mapping of genes to TSS’s: 1:Retrieve RNA-Pol RPKM within 1KB of each TSS and calculate the minimum of E9 and DMSO RPKMs. In case of the same gene with multiple TSS’s, only retain the gene record with the max RNA-Pol RPKM minimum. 2:In case of multiple genes with the same TSS, calculate the minimum FPKM between E9 and DSMO for each gene and only retain the gene with the max FPKM minimum
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq and whole genome sequencing WIG tracks were generated with deeptools v3.1.3 and normalized with the RPGC option

source_name: highly metastatic osteosarcoma cell line

extract_protocol:
For ChIP-Seq, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-Seq samples, cells were lysed and RNA extracted with TRIzol according to the manufacturer’s protocol.
ChIP-Seq libraries were prepared as previously described (Schmidt et al. 2009). For RNA-seq, Total RNA was treated with DNase I (Invitrogen, Carlsbad, CA). RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, Foster City, CA) and analyzed on an Agilent Bioanalyzer 2100 for integrity. PolyA+ RNA was isolated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol. For Whole Genome Sequencing, PCR-free libraries were prepared from MG63.3-GFP and 143B-GFP cells using TruSeq DNA PCR-Free High Throughput Library Prep Kit (Illumina, 20015963) and following the manufacturer’s instructions.

tag: cell line

tag: chip antibody


title: HC1__CD4-Tem cells

tag: tissue

value: Tem CD4 cell


title: LDT9C [S209]

value: dark cycling timepoint:light:dark, time point 9, replicate C


title: TEC ShCxD4 rep1

value: male

value: day 4 post sham-castration

tag: cell type

value: thymic epithelial cell (TEC)


title: MG63-3_E9_treated_rep2: RNA Seq

value: highly metastatic osteosarcoma cell line


title: HC1__CD4-Tcm cells

value: blood

value: Tcm CD4 cell

value: healthy

tag: age

value: M


title: TEC CxD7 rep1

value: day 7 post castration


title: MG63-3_E9_treated_rep1: RNA Seq


title: TEC Normal Aged rep2

value: middle-aged (9-12mo old)


title: TEC ShCxD4 rep2

value: 9-12 months old

value: thymus


title: LDT9A [S207]

value: Putnam et al. (2007)

value: dark cycling timepoint:light:dark, time point 9, replicate A


title: TEC Normal Aged rep1


title: MG63-3_DMSO_treated_rep3: RNA Seq


title: TEC Normal Young rep2

source_name: TEC Normal Young

value: young (5-6wk old)


title: TEC Normal Young rep1


title: TEC Normal Young rep3


title: DDT8D [S206]

source_name: dark:dark_time point 8_whole organism

value: dark cycling timepoint:dark:dark, time point 8, replicate D

value: adult


title: MG63-3_DMSO_treated_rep2: RNA Seq


title: LDT9B [S208]

value: dark cycling timepoint:light:dark, time point 9, replicate B


title: ATAC_CD8SP-WT

data_processing:
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads from Naive sample were randomly distributed into 2 subsamples
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Highly reproducible peaks were selected using an IDR cut-off=10%
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal

extract_protocol:
20000 (Naïve/TIM) or 50000 sorted cells washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.

value: Thymocytes

value: CD8SP WT


title: ATAC_CD8SP-EomesTG

value: CD8SP EomesTG


title: CD4_w0__R103_K5705: CD4 before treatment 6

source_name: CD4 T cell

extract_protocol:
Total RNA from were extracted using RNeasy Micro kit (Qiagen).
0.2 ng of total RNA from each dose and biological replicate were reverse transcribed to cDNA with SuperScript® VILO™ cDNA Synthesis Kit. Then cDNA is amplified using Ion AmpliSeq™ technology. After primer digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification. Libraries were then diluted to 75 pM and pooled equally, with eighteen individual samples per pool.

treatment_protocol: Frozen peripheral mononuclear cells were thawed, and CD4 and CD8 T cell were purified using FACS Aria Ⅲ.

tag: diagnosis

value: rheumatoid arthritis

value: CD4 T cell


title: CD4_w24__R259_K9021: CD4 after treatment 5

value: F


title: CD4_w24__R103_K7583: CD4 after treatment 6

value: M