title: ATAC-Seq Naive CD8 patient 0040

description:
Naive_CD8.LMC.208-30-0040.S11
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed


title: TDEC_S5_3

status: Public on Mar 30 2022

type: SRA

city: Okayama City

first: Nobushige

last: Tsuboi

state: Okayama Prefecture

address: 2-5-1 Shikata-cho Kita-ku

department: Neurological Surgery

country: Japan

institute: Okayama University

library_source: transcriptomic

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and bcl2fastq v2.19.  RTA3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v0.38, and mapped to mm10 whole genome using HISAT2 v2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts v1.6.3
Assembly: Filtered reads were mapped to mm10 using HISAT2 (v2.1.0).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: TDEC with Sertraline 5µM

growth_protocol: 005s were cultured or maintained with stem cell mentainance medium(FBS free). Tumor derived endothelial cells (TDEC) was differentiated from 005 with EGM-2 BulletKit  culture medium (Lonza, Basel, Swizerland) in hypoxic CO2 incubator (1% O2). Mouse brain microvascular endothelial cells (MBMEC) were purchased from Cell Biologics (Chicago, USA) and cultured in Complete Medium Kit With Serum and cultureBoost-R (4Z0-500-R, Cell systems, Kirkland, USA).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
NEBNext Poly(A) mRNA Magnetic Isolation Module(for PolyA selection), NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina (for strand specific library)

treatment_protocol: TDECs differentiated for 5 days from 005 were treated with 5 µM Sertraline and samples were collected 24 hours later.

tag: strain

tag: cell type

value: TDEC treated with Sertraline


title: TDEC_S5_1


title: ATAC-Seq Naive CD8 patient 0044

city: Umbilo

first: Werner

last: Smidt

state: KZN

address: 719 Umbilo Rd

country: South Africa

institute: African Health Research Insititute

description:
Naive_CD8.LMC.208-30-0044.S12
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed

library_source: genomic

data_processing:
ATAC-Seq reads were trimmed with trim_galore
ATAC-Seq reads were aligned to the hg19 genome with BWA
Peak calling was performed with MACS2 with an IDR threshold of 0.1
RNA-Seq data were quantified with Kallisto using Ensembl release 75 of the human transcriptome
Genome_build: hg19
Supplementary_files_format_and_content: bed, normalized tpm

molecule: genomic DNA

organism: Homo sapiens

source_name: Naive CD8 cells from Lymph Node

extract_protocol:
ATAC-Seq extraction protocol as described by Buenrostro et. al., 2013
ATAC-Seq libraries were constructed as described by Buenrostro et. al. 2013
Total RNA was isolated from lysed cells using Qiagen RANeasy mini columns
RNA-Seq libraries were prepared with the NEBNext ultra RNA library preparation kit

tag: tissue


title: Healthy control 2 [re-analysis]

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St

country: USA

institute: Yale School of Medicine

description:
Cont2 (re analysis of GSM4815799)
Cont2_S5_L001

data_processing:
Reads were aligned using HISTAT2 (version 2.1.0) against the Genome Reference Consortium Human Build 38 (hg38)
Quantification was done using RefSeq Transcripts release 93.
Quantified reads were normalized to log2(FPKM+1
Differentially expressed genes between control, pre-treatment, and during treatment groups, was carried out on Qlucore Omics Explorer (version 3.5, Qlucore AB, Lund, Sweden)
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38
Supplementary_files_format_and_content: Normalized_counts_bulkrna.csv

source_name: Skin

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini kits (Qiagen cat# 74704) according to the manufacturer’s instructions. Homogenization of the tissue was achieved using a rotor-homogenizer (PowerGen 125, ThermoFisher). .
RNA was submitted to the Yale Stem Cell Center and complementary DNA libraries were prepared and 100-base pair paired-end stranded sequencing was performed on an Illumina HiSeq 4000, also at Yale Stem Cell Center

treatment_protocol: Six patients with severe, long-standing sarcoidosis were enrolled and treated with tofacitinib monotherapy (5 mg twice daily) for 6 months. Concomitant methotrexate and/or low dose prednisone was allowed so long as the dose had been stable over the prior 3 months.

tag: subject status

value: healthy control

tag: treatment

value: skin


title: TDEC_S5_2


title: ATAC-Seq Naive CD8 patient 0052

description:
Naive_CD8.LMC.208-30-0052.S8
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed


title: MBMEC_2

source_name: MBMEC

value: mouse brain microvascular endothelial cell


title: L10_High_nutrition_fetal_liver

type: RNA

city: Tsukuba

first: Susumu

last: Muroya

state: Ibaraki

address: Ikenodai 2

department: Animal Products Research Division

institute: NARO Institute of Livestock and Grassland Science

description: Japanese Black cattle

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

molecule: polyA RNA

organism: Bos taurus

source_name: liver, high nutrition, 8.5-mo fetus

label_protocol: Cyanine-3 (Cy3) labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: According to the JFSC, the recommended contents of dry matter (DM), neutral detergent fiber, acidic detergent fiber, ash, crude protein (CP), Ca, and P in diet are 68.0, 56.1, 36.0, 11.1, 8.0, 0.6, and 0.3%, respectively (all values are expressed as a percentage of DM) . The cows randomly assigned to the LN (n = 5) and HN (n = 6) diet groups were fed the respective diet during gestation including prepregnant period. Metabolizable energy of the mixture feed for 100% requirement was estimated as 8.56 MJ/kg DM.

extract_protocol: Total RNA was extracted from the liver using the mirVanaTM microRNA isolation kit (Thermo Fisher Scientific), following the manufacturer’s instructions. The quantity and quality of the RNA were determined using an Agilent Bioanalyzer 2100 with an RNA 6000 Pico kit (Agilent Technologies)

treatment_protocol: The fetuses were euthanized by exsanguination at day 260 ± 8.3 of gestation after injecting 200 mg of lidocaine (AstraZeneca, Osaka, Japan) into the jugular vein. The liver was collected from the right side of the fetal carcass, frozen with liquid nitrogen or soaked in RNAlater (Thermo Fisher Scientific).

value: fetal liver tissue

tag: maternal nutrition status

value: High nutrition

tag: age

value: 8.5 months post-conception


title: MBMEC_3


title: Healthy control 1 [re-analysis]

description:
Cont1 (re analysis of GSM4815798)
Cont1_S4_L001


title: ATAC-Seq Naive CD8 patient 0054

description:
Naive_CD8.LMC.208-30-0054.S5
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed


title: ATAC-Seq Naive CD8 patient 0062

description:
Naive_CD8.LMC.208-30-0062.S5
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed: cd8.ln.naive.bed


title: Sarcoidosis patient 8 after treated with tofacitinib for six months [SAR6_du_pr]

description:
SAR6 du
SAR6_du_S28_L003

source_name: Lesional skin

value: Sarcoidosis patient

value: tofacitinib


title: Sarcoidosis patient 5 after treated with tofacitinib for six months [SAR5_du_pr]

description:
SAR5 du
SAR5_du_S26_L003


title: Sirt2_WT_3

city: Sapporo

first: Ryo

last: Hisada

state: Hokkaido

address: 3-11, Miyanomori, Tyuouku, Sapporo

institute: BIDMC Rheumatology and Clinical Immunology

data_processing:
Transcripts Assembly: Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 [2] to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/. The mapped reads of each sample were assembled using StringTie [3]. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie [3] and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Different expression analysis of mRNAs: StringTie [3] was used to perform expression level for mRNAs by calculating FPKM. mRNAs differential expression analysis were performed by R package DESeq2 [4] between two different groups (and by R package edgeR [5] between two samples). The mRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change > 2 were considered differentially expressed mRNAs.
Assembly: mm9
Supplementary files format and content: Gene and transcript differential expression in SIRT2 KO and Control Th17 cells
Supplementary files format and content: Go enrichment analysis in SIRT2 KO and Control Th17 cells

source_name: T cells

extract_protocol:
CRISPR/Cas9-enabled Sirt2 knockout and control Th17 cells were stimulated with anti-CD3 (0.5 μg/mL) and anti-CD28 (1 μg/mL) for 72 hours. Total RNA was extracted using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Th17 cells

value: untreated

tag: genotype

value: Sirt2 WT


title: Sarcoidosis patient 8 prior to treated with tofacitinib [SAR6_pr_pr]

description:
SAR6 pr
SAR6_pr_S27_L003


title: L3_High_nutrition_fetal_liver

description: Japanese Black cattle


title: L2_High_nutrition_fetal_liver

description: Japanese Black cattle


title: ATAC-Seq Naive CD8 patient 0068

description:
Naive_CD8.LMC.208-30-0068.S5
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed: cd8.ln.naive.bed


title: L8_Low_nutrition_fetal_liver

description: Japanese Black cattle

source_name: liver, low nutrition, 8.5-mo fetus

value: Low nutrition


title: L9_Low_nutrition_fetal_liver

description: Japanese Black cattle


title: 1stTDEC_3

source_name: TDEC

value: endothelial cell differentiated from 005


title: ATAC-Seq Naive CD8 patient 0074

description:
Naive_CD8.LMC.208-30-0074.S11
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.naive.bed


title: L1_High_nutrition_fetal_liver

description: Japanese Black cattle


title: 1stTDEC_2


title: Sarcoidosis patient 2 after treated with tofacitinib for six months [SAR4_du_pr]

description:
SAR4 du
SAR4_du_S24_L003


title: Sirt2_WT_2


title: Sirt2_WT_1


title: ATAC-Seq non-fcd8 patient 0037

description:
CXCR5_Neg_CD8.LMC.208-30-0037.S10
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed

source_name: Non-fCD8 cells from Lymph Node


title: 1stTDEC_1


title: L6_Low_nutrition_fetal_liver

description: Japanese Black cattle


title: Sarcoidosis patient 2 prior to treated with tofacitinib [SAR4_pr_pr]

description:
SAR4 pr
SAR4_pr_S23_L003


title: MBMEC_1


title: ATAC-Seq non-fcd8 patient 0040

description:
CXCR5_Neg_CD8.LMC.208-30-0040.S7
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed


title: Sirt2_KO_3

value: Sirt2 KO


title: 1st_TDEC_2days_3

source_name: TDEC day2

value: endothelial cell differentiated for 2 days from 005


title: Sirt2_KO_2


title: Sarcoidosis patient 7 after treated with tofacitinib for six months [SAR3_du_cr]

description:
SAR3 du
SAR3_du_S22_L003


title: 1st_TDEC_2days_2


title: ATAC-Seq non-fcd8 patient 0052

description:
CXCR5_Neg_CD8.LMC.208-30-0052.S4
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed


title: L5_Low_nutrition_fetal_liver

description: Japanese Black cattle


title: Sirt2_KO_1


title: Sarcoidosis patient 7 prior to treated with tofacitinib [SAR3_pr_cr]

description:
SAR3 pr
SAR3_pr_S21_L003


title: 1st_TDEC_2days_1


title: ATAC-Seq non-fcd8 patient 0054

description:
CXCR5_Neg_CD8.LMC.208-30-0054.S1
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed


title: Sarcoidosis patient B after treated with tofacitinib for six months [SAR2_du_cr]

description:
SAR2 du (previously published paper PMID 31916703)
SAR2_du_S20_L003


title: ATAC-Seq non-fcd8 patient 0068

description:
CXCR5_Neg_CD8.LMC.208-30-0068.S1
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed: cd8.ln.cxcr5_neg.bed


title: ATAC-Seq non-fcd8 patient 0074

description:
CXCR5_Neg_CD8.LMC.208-30-0074.S7
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_neg.bed


title: ATAC-Seq fCD8 patient 0037

description:
CXCR5_Pos_CD8.LMC.208-30-0037.S7
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed

source_name: fCD8 cells from Lymph Node


title: ChIP-Suz12_X1treatedl_1 [RAb5-4]

city: hopkinton

first: barry

middle: A

last: kesner

state: ma

address: 1 chamberlain street

institute: molecular biology

data_processing:
Adapters were removed from day 5 TST RNAseq library with software trim_galor/cutadapt (versions 0.4.3/1.7.1) with default parameters to remove adapters. Adapters were not removed from other libraries.  Mapping performed using software Novalign (version 3.09) or STAR (version STAR_2.5.3a) against the mouse C57BL/6J (mm9) as well as variants M. musculus (mus) and M. castaneus (cas), considering directional, first strand, for RNA-seq and unstranded reads for ChIP-seq.   Salient parameters for Novalign are -i300 100 -t180 -F ILM1.8 -rRandom -h180 180 -v180 and STAR are --outSAMprimaryFlag AllBestScore --outMultimapperOrder Random --outSAMtype BAM Unsorted --outFilterMultimapNmax 100 --outFilterMismatchNmax 6 --outSAMattributes All ?sjdbFileChrStartEnd.   Bigwig files were generated using inhouse software,  and read in the Integrative Genomics Viewer.
DEseq2 is used to quantitate RNA seq counts over genes using software Seq Monk (version 1.44.0 or greater).  We limited our analyses to highly expressed genes (RPKM > 1 in the DMSO control) and for cumulative distribution we set a liberal DEseq2 p-values (p<1) to see the general trend.  Plots were attained converting counts to log2 fold change in awk and then importing to R where ggplot2, stat_ecdf() and Wilcox.test were used to generate statistics.  For scatterplots comparing CHiP to RNA seq results, comp tracks were sampled to the smallest library, then MultiTesting and IndependentFiltering DESeq2 filtering is performed reporting significance below 0.05 after Benjamini and Hochberg correction with the application of independent intensity filtering, reporting shrank log2 values.
Metagene analysis of d5 tst cells of H3K27me3 and Suz12 marks is performed using the software ceas (version 1.0.2 under python 2.7) on FPM scaled coverage (wiggle format) generated over active genes plus or minus 3000 nt.  Highly expressed genes are used to avoid conflating repressed genes on Xa with those on Xi, and are defined as having FPKM greater than 1 in d5 tst cells strand specific RNA sequencing experiments. We used several equal methods to determine FPKM, including software packages SeqMonk and Homer (version 4.10). When we use the software package Homer we performed the following operations: tags directories are created from uniquely aligned reads to mm9 using makeTagDirectory tags with parameters -flip -sspe -removeSpikes 10000 8 -tbp 1 -genome mm9 -checkGC. Note effective removal of PCRd dups using tbp. The function AnalyzeRepeats is used to generate raw counts over genes.  FPKM values are derived scaling to gene length per 1000 and per million. Obtaining FPKM from SeqMonk is derived first using the RNAseq quantification pipeline to generate raw counts.  Then, quantitate existing probes using read count quantification choosing correct for total read count using per million reads and correct for probe length.ragments derived from uniquely aligned paired ends without PCR dups removed.
Additional ChIP analysis for comparing to RNAseq, is performed in Seq Monk using feature probe creation 5000 nt upstream of genes, read count quantification over these probes. For allelic analysis these values are scaled to the number of read per million in their associated comp library prior to log2 transformation and filtering out reads with very small counts.  For non-allelic analysis we did similar analysis however, after scaling the comp track, we used a script to subtract input replacing any values less than 0 with a pseudo count of 1e-5 to prevent divide by zero errors.  We then derived log2 fold change of treated over control.  The software R ggplot2 library is used to create plots.  Additionally, stat_compare_means is used to define p-values.
In addition, to obtain allelic skew of treated vs non-treated we used the metric (mus/(cas+mus)). This has the advantage that it is invariant to experiment size and therefore can be used to understand the relative enrichment of one allele over the other in a non-bias manner. We defined active genes as genes having FPKM > 0.5. In SeqMonk, we created groups that combined, for each replicate of RNA seq, each allelic type (cas and mus). Then, using the RNA-seq pipeline, we quantified raw probe counts within genes (merged transcripts isoforms) for both mus and the newly created groups. Then we obtained (mus/(cas+mus)) by using relative quantification, dividing each mus by its respective cas and mus group count. We obtained only values associated with chromosome X by creating a positional filter. Using the resulting X chromosome probes, we create an annotation report with exact overlapping genes. Finally, to compare the drug response in a way that is invariant to experiment size, using this report, we compared X1 treated to non-treated and counted genes that had a 10 percent increase in (mus/(cas+mus)) over non-treated. All performed under mac OS 10.14.6 using a late 2013 Macbook Pro.
Genome_build: mm9

source_name: day 5 ES cells

extract_protocol:
Growing embryoid bodies (EBs) were transferred to a gelatin-coated plate on day 4 and maintained for 24 hours more. Total RNA was obtained using an RNA-zol extraction kit from Zymo Research with DNase treatment. For ChIP experiments, EBs were cross-linked with 1% PFA for 10 minutes, quenched with 0.125 M glycine, and chromatin was extracted and sonicated to obtain 200-500 bp fragments.
5 million cells were crosslinked with 1% formaldehyde in 1x PBS for 10 min and lysed in Farnham lysis buffer (5 mM PIPES pH 8.0; 85 mM KCl; 0.5% NP-40) passing the lysate through a 19-gauge needle 20 times. Nuclei were collected at 400 rcf for 5 min and resuspended in RIPA buffer (1x PBS; 1% NP-40; 0.5% sodium deoxycholate; 0.1% SDS). Then, they were sonicated at 40% amplitude for 20 min (Qsonica, CT). Chromatin shearing between 150 and 500 pb was confirmed by 1% agarose gel electrophoresis. 25 ug of sample (A260 quantification) were combined with 5 ug of a Rabbit anti Suz12 (#39057, Active Motif, CA) or normal rabbit IgG bound to Dynabeads Protein A. Bead-antibody complexes were washed five times with IP wash buffer (100 mM Tris pH 7.5; 500 mM LiCl; 1% NP-40; 1% sodium deoxycholate), once with 1x TE, and DNA-proteins were eluted with 1% SDS; 0.1 M NaHCO3 for 1 h at 65°C. Crosslinking was reversed incubating the samples ON at 65°C. The next day, DNA was purified using the QIAquick PCR purification kit (Qiagen, Germany) and quantified for library preparation using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher).
Total RNA isolated as described above and ChIP samples for sequencing were prepared using NEBNext library preparation kits from New England Biolabs. Poly(A) RNAs were isolated from RNA samples using the Poly(A) mRNA Magnetic Isolation Module (NEB). The first cDNA strand was obtained using Superscript III in presence of Actinomycin D, and the second cDNA strand was obtained using the Ultra Directional RNA Second Strand Synthesis module (NEB). From this point, both RNA- and ChIP-derived samples followed the same protocol: double stranded DNA was end-repaired, dA-tailed, adaptor-ligated and size-selected using the ChIP-seq library prep master mix set for Illumina (NEB). Size of the libraries was confirmed using high sensitivity DNA reagents for Bioanalyzer (Agilent, CA) and sample concentration was determined using the KAPA library quantification kit (Kapa Biosystems, MA). Libraries were sequenced in Illumina HiSeq sequencer.

treatment_protocol: Mouse female stem cells (Ogawa et al., 2008) were induced to differentiate in suspension by LIF depletion. 10 uM drug or vehicle (DMSO) were added from day 2 and replenished every day.

value: TST cells

tag: timepoint

tag: chip antibody

value: rabbit anti Suz12 (#39057, Active Motif)


title: Sarcoidosis patient B prior to treated with tofacitinib [SAR2_pr_cr]

description:
SAR2 pr (previously published paper PMID 31916703)
SAR2_pr_S19_L003


title: Sarcoidosis patient A after treated with tofacitinib for six months [SAR1_du_cr]

description:
SAR1 du (previously published paper PMID 30586518)
SAR1_du_S18_L003


title: 1st005_1

value: mouse glioma stem cell


title: ChIP-input_X1treated_1 [RAb5-3]

value: none; input


title: Sarcoidosis patient A prior to treated with tofacitinib [SAR1_pr_cr]

description:
SAR1 pr (previously published paper PMID 30586518)
SAR1_pr_S17_L003

value: skin


title: ATAC-Seq fCD8 patient 0040

description:
CXCR5_Pos_CD8.LMC.208-30-0040.S4
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed


title: ChIP-Suz12_DMSO_1 [RAb5-2]

value: DMSO


title: 1st005_2


title: AR2359 (FOX-069-001 low)

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at low glucose culture condition
TOLOSA_04

data_processing:
RNA-seq reads were mapped against human reference genome (GRCh38) using STAR software version 2.5.1b  with ENCODE parameters.
Genes were quantified using RSEM version 1.2.28  with default parameters and annotation file from GENCODE version 24
Differential expression analysis was performed with DESeq2 v1.18. R package  adjusting by sex on the model and using the Wald test to compare the experimental conditions
Genome_build: GRCh38 (primary assembly, gencode version 24)
Supplementary_files_format_and_content: raw counts (tsv)

source_name: fibroblasts

growth_protocol: Skin biopsies were obtained from sporadic and genetic forms of Parkinson’s disease and healthy controls. Fibroblasts were cultured in two conditions, high (25 mM) and low (5mM) glucose (DMEM; Gibco), and supplemented with 10% calf serum (CS) (Gibco) penicillin 100 U/mL, streptomycin 100 μg/mL, and heparin 125 μg/mL U/mL (DMEM/10% CS) (all Sigma, St Louis, Mo). Cells were grown at 37°C in 10% carbon dioxide and were passaged at confluence with a solution of trypsin/EDTA (Sigma).

extract_protocol:
RNA was performed using the Allprep DNA RNA Protein Minikit from Quiagen following manufacter instructions. Starting material included three times PBS washed cellular pellets of 106 cells. DNA and RNA concentration were determined on a NanoDrop ND-3300 Fluorospectrometer, and RNA integrity was examined with the Bioanalyzer 2100 (Agilent).
RNA sequencing (RNA-seq) was performed at the Centro Nacional de Análisis Genómico (CNAG) in Barcelona, Catalonia. The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,) with minor modifications.

tag: disease state

value: healthy control

value: fibroblasts

tag: glucose

value: low 5 mM

tag: gender

value: male

tag: batch


title: ChIP-input-DMSO_1 [RAb5-1]


title: 1st005_3


title: RNAseq_NPC_0h_DMSO_rep3

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: RNA sequencing of NPCs

data_processing:
Raw reads were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC), followed by poly-A trimming with cutadapt (parameters: --overlap 20 --minimum-length 25 --adapter "A{100}" --adapter "T{100}").
Reads were aligned to the mouse reference (mm10) using STAR (version 2.7.5a; parameters: --runMode alignReads --chimSegmentMin 20 --outSAMstrandField intronMotif --quantMode GeneCounts) and transcripts were assembled using stringtie (version 2.0.6; parameters: -e) with GENCODE annotation (VM19).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file containing gene abundances: <Gene ID> <Gene Name> <Reference> <Strand> <Start> <End> <Coverage> <FPKM> <TPM>

source_name: NPC

growth_protocol: Cells were cultured on PDL/Laminin-coated dishes in RHB-A medium (Takara-Clontech, #Y40001) + bFGF (Thermo, #PHG0261)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) including the DNaseI treatment, following manufacturer's protocol
1 ug of RNA was used to prepare sequencing libraries with TrueSeq Stranded mRNA capture library prep kit (Roche) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 1:2000 DMSO


title: ATAC-Seq fCD8 patient 0054

description:
CXCR5_Pos_CD8.LMC.208-30-0054.S10
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed


title: AR2358 (FOX-076-001  low)

treatment_protocol: Fibroblasts were cultured in two conditions, high (25 mM) and low (5mM) glucose (DMEM; Gibco)

value: female


title: AR2357 (CTRL-003 low)


title: AR2356 (CTRL-002 low)


title: RNAseq_control_2 [CRa4-4]

value: d5 TST

value: d5 TST DMSO


title: RNAseq_NPC_0h_DMSO_rep2

description: RNA sequencing of NPCs


title: RNAseq_treated_2 [CRa4-3]

value: d5 TST X1 treated


title: RNAseq_NPC_0h_DMSO_rep1

description: RNA sequencing of NPCs


title: RNAseq_ESC_parental_rep3

description: RNA sequencing of mESCs

source_name: mESC

growth_protocol: mES cells were cultured in Knock Out DMEM media (Gibco) supplemented with 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF. Dishes were coated with 0.2 percent gelatin and plated with irradiated CD1 mouse embryonic fibroblasts (MEFs) as a confluent layer of feeder cells for ES cell maintenance. 50,000 mES cells were seeded per well of a six-well plate and were split every 3–4 days.

treatment_protocol: No treatment

value: no treatment


title: RNAseq_ESC_parental_rep2

description: RNA sequencing of mESCs


title: ATAC-Seq fCD8 patient 0074

description:
CXCR5_Pos_CD8.LMC.208-30-0074.S4
processed data file: cd8.ln.cxcr5_pos.bed


title: RNAseq_control_1 [CRa4-1]


title: ATAC-Seq fCD8 patient 0068

description:
CXCR5_Pos_CD8.LMC.208-30-0068.S10
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed


title: RNAseq_ESC_parental_rep1

description: RNA sequencing of mESCs


title: AR2354 (IPD-008 low)

value: sporadic Parkinson's disease


title: ATAC-Seq fCD8 patient 0052

description:
CXCR5_Pos_CD8.LMC.208-30-0052.S1
processed data file: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed: cd8.ln.cxcr5_pos.bed


title: RNAseq_treated_1 [CRa4-2]

value: d5 TST  X1 treated


title: AR2353 (SP-08 low)


title: AR2355 (CTRL-001 low)


title: ChIP-input_X1treated_1 [RAb3-3]

value: TST cells

tag: antibody

value: d5 TST input


title: Tumor_Ren_2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

source_name: Myc;p53-/- Liver Tumor, shRenilla

growth_protocol: In preparation for the procedure, the mouse is carefully warmed with a heat lamp to cause vasodilation. The needle is directed into a lateral tail vein at an angle of approximately 20o. Once the vein has been penetrated (preferably midway down the tail), the needle will be directed cranially a distance of approximately 2mm. Sterile 0.9% NaCl solution containing 5 µg of DNA of pT3-EF1a-Myc and 20 µg of CRISPR plasmid px330 DNA expressing Cas9 and single guide RNA (sgRNA) targeting either p53 or Axin1 together with CMV-SB13 Transposase (1:5 ratio) for each injection is administered in 5-7 seconds. Pressure is applied over the injection site after the needle is withdrawn from the vein for approximately 30 seconds with gauze (or similar material).Tumor formation was assessed by ultrasound imaging and RNA was collected from whole tumor or healthy tissue.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Mice harboring tumors measuring 50-100 mm3 were fed with a Dox diet to systemically induce the Cdk9 shRNA and control shRNA.

value: Whole Liver

value: Doxycycline Diet

value: Myc;p53-/- , shRenilla


title: ChIP-H3K27me3_X1treated_1 [RAb3-4]

value: d5 TST H3K27 IGG IP


title: Tumor_CDK9_1

source_name: Myc;p53-/- Liver Tumor, shCdk9

value: Myc;p53-/- , shCdk9


title: Tumor_Ren_1


title: Tumor_CDK9_2


title: ChIP-input-DMSO_1 [RAb3-1]


title: Normal_2

source_name: Normal Liver Tissue

value: Normal


title: RNAseq_ESC_shREPEATS_dTAG13_Dox_24h_rep2

description: RNA sequencing of mESCs

extract_protocol:
Lysates were prepared with RLT buffer (QIAgen Rneasy micro kit)
Libraries were constructed from 1ug of Total RNA using KAPA Hyperprep stranded Total RNAseq kit (with Riboerase HMR)

treatment_protocol: Cells were pre-treated with 2ug/mL concentration of Doxycycline for 24 hours prior to treatment with dTAG-13 (500nM) and 2ug/mL Doxycycline

tag: cell line

value: dTAG + Dox


title: RNAseq_ESC_shREPEATS_dTAG13_Dox_24h_rep3

description: RNA sequencing of mESCs


title: ChiP-H3K27me3  [RAb3-2]


title: RNA: DP T cell

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: 5’ Gene Expression Library

data_processing:
We used Cell Ranger v3.1.0 (10X Genomics) pipeline for FASTQ file generation from raw sequencing data.
Illumina basecall files from Illumina sequencing instrument were converted to FASTQ format for each sample using the ‘mkfastq’ command.
Sequencing reads were aligned to the Mmul_10 genome reference for Macaca mulatta using STAR (v2.5.1b) aligner. Those of feature barcoded libraries were matched to the target feature barcode reference.
gene and cell surface protein expression profiling in each cell was performed with the information of unique molecular identifier (UMI) and 10X cell barcode. Then, cells were grouped into clusters by their gene expression.
Raw count matrices of 10x genomics were imported to Seurat 3.1.3.
Assembly: Mmul_10
Supplementary files format and content: The lists of cell barcode and features in tsv format, filtered gene matrix table with raw gene counts in mtx and HDF5 format.

organism: Macaca mulatta

source_name: circulating CD4+CD8+ double positive T cells

extract_protocol:
CD4+ T cells were first separated from fresh PBMC using the REAlease CD4 MicroBead kit  according to the manufacturer's instructions. And then, CD4+CD8+ DP T cells were separated from isolated CD4+ T cells using CD8 Microbeads kit.
Libraries were prepared using the Chromium controller according to the 10x Chromium Single Cell V(D)J User Guide (10x Genomics).

value: Periperal blood

value: 6 years old

value: untreated

tag: molecule subtype

value: polyA RNA (mRNA)


title: AR2350 (FOX-019-001 low)

value: LRRK2 Parkinson's disease (G2019S mutation)

value: fibroblasts

value: low 5 mM

value: female


title: AR2352 (FOX-015-001 low)

value: sporadic Parkinson's disease

value: male


title: AR2351 (FOX-075-001 low)


title: AR2349 (FOX-069-001 high)

description:
fibroblasts RNA seq comparison of controls versus Parkinson's disease at high glucose culture condition
TOLOSA_04

value: healthy control

value: high 25 mM


title: FB:  DP T cell

description: Cell Surface Protein Library

value: circulating CD4+CD8+ double positive T cells

value: CD4, CD8 cell surface protein


title: AR2348 (FOX-076-001 high)


title: RNAseq_ESC_shREPEATS_dTAG13_Dox_24h_rep1

description: RNA sequencing of mESCs


title: F

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 17 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 15, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma Type I GT1 strain (ToxoDB-46, GT1 genome) as reference template.
The ArrayStar module (version 17, DNASTAR. Madison, WI, USA) was used for normalization, variant detection and statistical analysis of uniquely mapped paired-end reads using the default parameters.
Variant calls were filtered to select variants present in coding regions with the following criteria: variant depth ≥ 30, Q call ≥ 60, and absent in the parental wild-type strain. SNVs, insertions and deletions present in regulatory or intergenic regions were filtered out as they are unlikely to contribute to drug resistance.
For the expression data quantification and normalization, the FASTQ reads were aligned in parallel to the ToxoDB-46 build of the Toxoplasma gondii GT1 genome (ToxoDB-46) using Subread version 2.0.1 (Liao et al., 2013) with the following options ‘subread-align -d 50 -D 600 --sortReadsByCoordinates’. Read counts for each gene were calculated using featureCounts from the Subread package (Raw counts, in the Matrix table processed data).
Transcripts were quantified and normalized using the BAM files generated by Subread and TPMCalculator (TPM, in the Matrix table processed data).
Genome_build: Toxoplasma Type I GT1 strain (ToxoDB-46, GT1 genome).
Supplementary_files_format_and_content: xlsx format. The matrix table includes RNA-Seq report, raw counts and TPM values of T. gondii transcripts for each sample. Variants detected in each strain when compared to the GT1 reference genome are also provided.

organism: Toxoplasma gondii RH

source_name: HFF and parasites

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
18 hours post-infection, cells were harvested and total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

tag: t. gondii strain and genotype

value: RH, mutant F

tag: strain background

value: RH

tag: host cell type

value: Human HFF Cells


title: E

value: RH, mutant E


title: RNAseq_ESC_shREPEATS_dTAG13_24h_rep2

description: RNA sequencing of mESCs

treatment_protocol: Cells were pre-treated with 2ug/mL concentration of Doxycycline for 24 hours prior to treatment with dTAG-13 (500nM)

value: dTAG


title: HiC_tumor_Bcl6_Smc3_rep3

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

description:
In situ HiC
HiC_tumor_Bcl6_Smc3_merged.hic

data_processing:
Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the mm10 reference sequence using bowtie2 (special parameters: --very-sensitive-local --local).
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<5 kb).
.hic files: we created .hic files with juicer version 1.8.9 after merging all replicates.
Matrix generation: HicBench. For each sample and each chromosome, a matrix with binned interactions (bin-size 20kb) was generated.
Loops: Loop calling was performed similar as described in the Mango analysis approach after pooling all replicates. We applied a negative binomial test for all interactions of a chromosome at the same distance, corrected for multiple testing (FDR) and called significant loops at FDR<0.01 and CPM>30.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .hic files

source_name: Mesenteric lymph node tumor cells

extract_protocol: As per the Hi-C protocol (Rao et al., Cell 2017).

tag: cell type

value: Mesenteric lymph node tumor cells

value: C57BL/6 Bcl6/Smc3

tag: enzyme

value: DpnII


title: e17_5

city: Baltimore

first: Qin

last: Bian

address: 733 N Broadway

institute: Johns Hopkins University

description: paired

data_processing:
Demultiplexing was performed based on the 8 bp sample index read to generate FASTQs for the Read1 and Read2 paired-end reads.
Reads were aligned using STAR as implemented in the CellRanger pipeline
Barcodes and UMIs were filtered.
PCR duplicates were marked if two sets of read pairs shared a barcode sequence, a UMI tag, and a gene ID (Ensembl).
Previously described processing is according to: Zheng et. al. 2017.
Genome_build: mm10 with added exogenous genes including green fluorescent protein
Supplementary_files_format_and_content: There are two anndata (annotated data matrix) h5ad files. The file contains the preprocessed and annotated count data. annData_GLE_cells.h5ad contains the joint cells. annData_nonjoint_cells.h5ad contains the non-joint cells, such as blood cells, neural crest derivatives, and muscle.
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file
Supplementary_files_format_and_content: Note that Velocyto was used to estimate spliced and unspliced transcription counts for analysis presented in the paper and included in the H5AD files here.

source_name: embryonic hindlimb

growth_protocol: Mice were kept in light-reversed room (light turns on at 10 pm and turns off at 10 am).

extract_protocol:
The presumptive knee joints were isolated by transfemoral and transtibial division in a single 3 cm dish (Figure 1A) and incubated in digestion solution I (3 mg / mL collagenase D, DMEM high glucose culture medium, serum free) for 45 min at 37 °C, and then in digestion solution II (1 mg / mL collagenase D, DMEM high glucose culture medium, serum free) for 3 hrs (one embryo per dish) at 37 °C. During the period of incubation, the mice gender was identified by genotyping and only male samples were chosen for further processing. The tissues with medium were gently pipetted to disperse cell aggregates and filtered through 40 µm cell strainer, then centrifuged for 10 min at 400 g. The pellet was suspended with 0.4% BSA in PBS. Cells were subjected to FACS and YFP+ cells were collected for 10X sequencing.
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 30 Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) as indicated in Zheng et al 2017) .

treatment_protocol: Timing was determined by putting one male mouse and two female mice in the same cage at 9 am and separating them at 4 pm on the same day. We count that midnight as E0.5 stage. On E17.5 the pregnant mice were sacrificed by CO2 at 3 am. The cells were isolated using the protocol (Primary culture and phenotyping of murine Chondrocytes) with modification: The embryos (usually n=6-8) were rinsed three times in PBS on ice.

tag: tissue

value: hind limb

tag: Stage


title: RNAseq_ESC_shREPEATS_DMSO_24h_rep2

description: RNA sequencing of mESCs

treatment_protocol: Cells were pre-treated with 2ug/mL concentration of Doxycycline for 24 hours prior to treatment with DMSO (1:500)

tag: treatment

value: DMSO


title: Normal_1

value: Whole Liver

value: Doxycycline Diet

tag: genotype

value: Normal


title: RNAseq_ESC_shREPEATS_dTAG13_24h_rep1

description: RNA sequencing of mESCs


title: RNAseq_ESC_shREPEATS_DMSO_24h_rep3

description: RNA sequencing of mESCs


title: HiC_tumor_Bcl6_Smc3_rep4


title: AR2347 (CTRL-003 high)

value: healthy control

value: fibroblasts

value: female


title: RNAseq_ESC_shREPEATS_dTAG13_24h_rep3

description: RNA sequencing of mESCs


title: A

value: RH, mutant A


title: HiC_tumor_Bcl6_rep3

description:
In situ HiC
HiC_tumor_Bcl6_merged.hic

value: C57BL/6 Bcl6


title: AR2346 (CTRL-002 high)

value: high 25 mM


title: RNAseq_ESC_shREPEATS_DMSO_24h_rep1

description: RNA sequencing of mESCs


title: C

value: RH, mutant C

value: RH

value: Human HFF Cells


title: HiC_tumor_Bcl6_Smc3_rep2

value: Mesenteric lymph node tumor cells


title: AR2342 (FOX-015-001 high)

value: sporadic Parkinson's disease

value: male


title: B

value: RH, mutant B


title: HiC_tumor_Bcl6_Smc3_rep1

value: C57BL/6 Bcl6/Smc3

value: DpnII


title: HiC_tumor_Bcl6_rep2

description:
In situ HiC
HiC_tumor_Bcl6_merged.hic


title: Sample 6_Grafted_cornea_pbscontrol

city: Bunkyo-ku

first: Takenori

last: Inomata

state: Tokyo

address: 3-1-3 Hongo

institute: Juntendo University Graduate School of Medicine

description: Sample 6

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Trimmomatic (version 0.39) was used to remove adapters and filter raw reads <35 bases, as well as leading and trailing bases with quality <20.
Filtered reads were mapped to the sequence of the mouse genome (GRCm38) using HISAT2 (v2.1.0).
Raw counts for each gene were obtained using featureCounts software included with the Subread package with the default option (-p -t exon).
RUVSeq (version 1.18.0) was used for further normalization to account for sample variations.
Genome_build: mouse genome (GRCm38)
Supplementary_files_format_and_content: raw counts

source_name: Cornea

growth_protocol: Six-to 8-week-old BALB/c (H-2d), C57BL/6 (H-2b) male mouse (B6) were purchased from Sankyo Labo Service Corporation, Inc. (Tokyo, Japan) and housed in a pathogen-free animal room.

extract_protocol:
Two weeks after corneal transplantation, corneal grafts were excised and immediately submerged in the RNAlater solution (Ambion, Austin, TX, USA). Total RNA was isolated from five corneas each group by using a NucleoSpin RNA isolation kit (Macherey-Nagal GmbH, Duren, Germany).
The cDNA sequencing libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First and second strand cDNA synthesis were subsequently performed. The universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated on the Agilent TapeStation System (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were sequenced as 2x150 Paired End (PE) using the Illumina NovaSeq instrument according to manufacturer’s instructions.

treatment_protocol: The recipient mice were administrated intraperitoneally (i.p.) with 50 ug anti-CD80 and anti-CD86 mAb, reconstituted in totally 100 uL normal saline for each injection. The injection was performed at 0, 1, and 2 days after grafting (n = 5, each).

tag: host

value: Recipient; BALB/c

tag: strain

value: Graft; C57BL6

value: Cornea

tag: age

value: 12-14 week old

value: Wild type

value: PBS control


title: AR2344 (IPD-008 high)

tag: disease state

value: fibroblasts

tag: glucose

tag: gender

value: female


title: Sample 5_Grafted_cornea_pbscontrol

description: Sample 5


title: HiC_tumor_Bcl6_rep4

description:
In situ HiC
HiC_tumor_Bcl6_merged.hic

value: C57BL/6 Bcl6


title: RAJI U2 (11.4)

city: Badalona

first: Marcelo

middle: Lima

last: Ribeiro

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Leukaemia Research Institute (IJC)

data_processing:
The original raw data from Illumina platform are transformed to Sequenced Reads by base calling using CASAVA, performed by NOVOGENE Inc.
We used FASTQC (MAPq to merge all 24 runs) and FASTP for filtering to removie reads containing adapters, reads containing N > 10% and reads containing low quality (Qscore<= 5) base.
Gene expression was estimated using Salmon software (parameters -l A –validateMappings -p 2)
Assembly: hg19
Supplementary files format and content: Matrix table with normalized gene abundance for every gene and every sample. Data normalized using transcripts per million (TPM)

source_name: BL xenograft - RAJI

growth_protocol: NOD/SCID IL2Rγ-null (NSG) mice were subcutaneously injected with Raji cells and tumour-bearing mice were randomly assigned to the treatments. Representative bulk Raji xenografts with > 95% tumour B cells were collected

extract_protocol:
Purified CD20+ cells, together with representative Raji xenografts were subjected to RNA extraction and qPCR validation. Briefly, total RNA was extracted using TRIZOL (Thermo Fisher) following manufacturer’s instructions.
After the quality control procedures, mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume

treatment_protocol: TG-1801 (5 mg/kg, qw), ublituximab (5 mg/kg, qw) + umbralisib (150 mg/kg, bid), TG-1801+umbralisib combo or the triplet (U2 + TG-1801), or an equal volume of vehicle for 17 days.

value: BL xenograft

value: U2 combination


title: AR2340 (FOX-019-001 high)

value: LRRK2 Parkinson's disease (G2019S mutation)

value: high 25 mM

tag: batch


title: D

value: RH, mutant D

value: RH

value: Human HFF Cells


title: AR2343 (SP-08 high)

value: sporadic Parkinson's disease


title: RAJI 1801 (1.2)


title: Sample 4_Grafted_cornea_pbscontrol

description: Sample 4

value: Recipient; BALB/c


title: RAJI COMBO (10.1)

value: Triplet combination


title: AR2345 (CTRL-001 high)

value: healthy control

value: male


title: Sample 3_Grafted_cornea_anticd8086

description: Sample 3

value: Graft; C57BL6

value: Cornea

value: 12-14 week old

value: Wild type

value: CD80/86 antibodies injection


title: EL4 GFP + GATA3 rep2

city: London

first: Arnulf

last: Hertweck

address: Gower Street

department: UCL Cancer Institute

country: United Kingdom

institute: University College London

data_processing:
Raw reads were ﬁltered for base quality using FastQC with default parameters and adapters sequences were removed with Trim Galore!
Transcript-level read abundances were created with kallisto using the Gencode M20 transcript models
Genome_build: mm10
Supplementary_files_format_and_content: kallisto transcript level abundaces tab-delimited text files

source_name: EL4 cell line

growth_protocol: EL4 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 4 mM L-alanyl-L-glutamine, 25 mM D-glucose, 1 mM sodium pyruvate, 10 mM HEPES, 100 U/ml penicillin and 100 µg/ml streptomycin

extract_protocol:
Total RNA was isolated with TRIsure (Bioline)
Poly-adenylated RNA was purified from 1 mg of total RNA using the Qiagen Oliogtex kit and ribosomal RNA was depleted from total RNA using Ribo-Zero Gold (EpiCentre), as per manufacturers instructions. 5’ cap structures were removed with tobacco acid pyrophosphatase (TAP, Life Technologies) and RNA fragmented with potassium acetate (100mM) and magnesium acetate (30mM) at 94oC for 3 mins. RNA was then repaired with Antartic phosphatase and PNK, according to the instructions in the Illumina Directional mRNA-Seq Sample Prep Guide.

treatment_protocol: EL4 cells were stimulated with phorbol 12-myristate 13-acetate (50 ng/ml) and ionomycin (1 μM) for 4 hours prior to RNA extraction

tag: cell line

value: PMA  + inomomycin

tag: ectopically expressed protein


title: EL4 T-bet + GATA3 rep2

value: FLAG-T-bet + HA-GATA3


title: Sample 1_Grafted_cornea_anticd8086

description: Sample 1

tag: graft strain


title: AR2341 (FOX-075-001 high)

value: LRRK2 Parkinson's disease (G2019S mutation)

value: fibroblasts


title: HiC_tumor_Bcl6_rep1

description:
In situ HiC
HiC_tumor_Bcl6_merged.hic

value: Mesenteric lymph node tumor cells

value: C57BL/6 Bcl6

value: DpnII


title: WT

tag: t. gondii strain and genotype

value: RH, wild-type

tag: strain background

value: RH

tag: host cell type

value: Human HFF Cells


title: RAJI Control (15.2)

tag: cell type

value: BL xenograft

value: untreated


title: RAJI U2 (4.3)

value: U2 combination


title: RAJI COMBO (10.3)

value: Triplet combination


title: EL4 T-bet + Plum rep2

value: FLAG-T-bet


title: HiC_ESC_DMSO_rep2

description: Hi-C from mESCs

data_processing:
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC).  Technical replicates of treatment samples were merged respectively using samtools 'merge'. Reads were further trimmed at MboI restriction site using cutadapt (version 2.4; parameters: -a GATC, --minimum-length 25) and separately aligned to the mouse genome (mm10) using BWA ‘mem’ (version 0.7.17, default parameters). Rest of Hi-C data processing was performed with HOMER software (version 4.10).  Paired-end reads were matched and prepared for analysis with ‘makeTagDirectory’ and PCR duplicates were removed (parameters: -tbp 1). Reads were filtered to remove continuous genomic fragments, re-ligation events, self-ligations and tags from regions with unusually high tag density while keeping only paired-end reads where both reads have a MboI restriction site within the fragment length estimate 3’ to the read (parameters: -removePEbg -restrictionSite GATC -both -removeSelfLigation -removeSpikes 10000 5). Conversion to .hic format was performed with ‘tagDir2hicFile.pl’ using 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb and 1Mb resolutions.
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C matrices in .hic format from merged replicates

growth_protocol: During expansions, cells were cultured on irradiated primary mouse embryonic fibroblasts (MEFs) under serum/LIF conditions: knockout DMEM containing 15 % fetal bovine serum,  50 µg/ml penicillin/streptomycin, 2 mM L-Glutamine, 100 µM non-essential amino acids, 80 µM ß-mercaptoethanol and 1000 U/ml LIF. Before starting Hi-C experiments, mESCs were depleted from MEFs by incubating them on gelatin coated cell culture plates for 45 min in +37 C allowing MEFs to attach while mESCs remain in suspension. MEF depletion was performed two times after which mESCs were seeded on gelatin coated plates and maintained in serum/LIF conditions with 2000 U/ml LIF.

extract_protocol: Three million cells per sample were fixed in suspension with 1 % formaldehyde for 10 minutes and quenched with 0.125 M glycine for 5 minutes in rotation. Cells were washed with PBS and lysed in Hi-C lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% Igepal CA-630, 1.15 % Triton X-100 and 1x protease inhibitors (Roche)) for 10 minutes on ice. Nuclei were washed with cold PBS, NEBuffer 2 (NEB) and resuspended in 50 µl of 0.5 % SDS, incubated in 62 °C for 7 minutes and SDS was quenched with 145 µl water and 25 µl 10 % Triton X-100 followed by 15 min incubation in 37 °C. For restriction enzyme digestion, 25 µl of 10X NEBuffer2 and 250 U of MboI (NEB) were added and samples were incubated overnight in 37 °C, followed by additional 1 hour incubation after adding another 250 U of MboI. Enzymes were inactivated for 20 minutes in 65 °C. Samples were spinned in 5000 g, 200 µl of supernatant was removed and sample was resuspended in 200 µl of 1.2X NEBuffer 2. To fill-in DNA overhangs, 50 µl of fill-in buffer (37.5 µl of 0.4 mM biotin-14-dATP (Thermo Fisher, 19524016), 1.5 µl of dCTP, 1.5 µl of dGTP, 1.5 µl of dTTP, 10 mM each, and 8 µl of 5U/µl DNA PolI Large (Klenow) Fragment (NEB)) was added and the samples were incubated in 37 °C for 90 minutes. For ligation reaction, samples were topped up with 663 µl of water, 120 µl of NEB T4 DNA ligase buffer (NEB), 100 µl of 10 % Triton X-100 and 12 µl of 10 mg/ml BSA (NEB) and 2000 U of T4 DNA ligase (NEB) and incubated overnight in 18 °C in rotation. Crosslinks were reversed with Proteinase K and 0.88 % SDS in 10 mM Tris-HCl (pH 7.5) during 30 min in 55 °C, followed by incubation in 68 °C in presence of 2.3 M NaCl for 2 hours. For library preparation, DNA was extracted from samples with ethanol and sodium acetate precipitations, sheared with Covaris E220 and pulled down with 150 µl of T1 Streptavidin Dynabeads (Thermo Fisher). The end-repair for captured DNA was performed in room temperature for 30 minutes using 100 µl reaction with 0.5 U of T4 Polynucleotide Kinase (NEB), 12 U of T4 DNA polymerase (NEB) 5 U of DNA pol I Large (Klenow) Fragment in NEB T4 DNA ligase buffer with 10 mM ATP and 0.5 mM dNTP. After washing the bead-bound DNA, samples were resuspended to NEBuffer 2 with 0.5 mM dATP and 25 U of Klenow exo minus (NEB) and incubated in 37 °C for 30 minutes. After washing the beads, universal sequencing adapters from NEBnext Ultra DNA Library Kit (NEB) were ligated in NEB Quick ligation reaction buffer according to manufacturer’s guidelines. Libraries were amplified for 6 PCR cycles and purified using Ampure XP beads (Beckman Coulter). Libraries were paired-end sequenced with NovaSeq 6000 for 400 million fragments for each library.

treatment_protocol: For degradation of TRIM28, 500 nM of dTAG-13 (or 0.05 % DMSO) was mixed with mESC medium and added to the cells 24h before samples were collected.

value: mESC

value: DMSO


title: HiC_ESC_dTAG_24h_rep1

description: Hi-C from mESCs


title: Sample 2_Grafted_cornea_anticd8086

description: Sample 2

value: Recipient; BALB/c

value: Graft; C57BL6

tag: tissue

value: Cornea

value: 12-14 week old

value: Wild type

value: CD80/86 antibodies injection


title: EL4 GFP + Plum rep2

tag: treatment

value: PMA  + inomomycin


title: RAJI Control (13.0)


title: RAJI 1801 (1.0)


title: HiC_ESC_DMSO_rep1

description: Hi-C from mESCs


title: HiC_ESC_dTAG_24h_rep2

description: Hi-C from mESCs


title: f2_tg_hfd_male_RNA_rep3

city: Sainte-Anne-de-Bellevue

first: Anne-Sophie

last: Pépin

state: QC

address: 21111 Lakeshore road

department: Department of Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
ChIP:Sequencing reads were trimmed using Trimmomatic on single-end mode to remove adapters and filter out low-quality reads (version 0.36, parameters: 2:30:15 LEADING:30 TRAILING:30) (Bolger, Lohse and Usadel, 2014). Trimmed reads were aligned to the Mus Musculus mm10 genome assembly using Bowtie2 (version 2.3.4) (Salzberg, 2013). Unmapped reads were removed using SAMtools (version 1.9) (Li et al., 2009), and those with 3 mismatches or more were filtered out using Perlcode. BAM coverage files (BigWig) were generated using deeptools2 bamCoverage function (version 3.2.1, parameters: -of bigwig -bs 25 -p 20 --normalizeUsing RPKM -e 160 --ignoreForNormalization chrX) (Ramírez et al., 2016).
RNA: Reads were trimmed using Trim Galore (version 0.5.0, parameters for HiSeq: --phred33 --length 36 -q 5 --stringency 1 -e 0.1; parameters for NovaSeq: --paired --retain_unpaired --phred33 --length 36 -q 5 --stringency 1 -e 0.1) (Krueger, 2015). Trimmed reads were aligned to the Ensembl Genome Reference Consortium mouse reference 38 (GRCm38) primary assembly using hisat2 (version 2.1.0, parameters: -p 8 --dta) (Kim, Langmead and Salzberg, 2015). Aligned files with SAM format were converted to binary SAM format (BAM) and sorted by genomic position using SAMtools (version 1.9) (Li et al., 2009). Transcripts were assembled and gene abundances calculated using Stringtie (version 2.1.2, parameters: -p 8 -e -B -A) (Pertea et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, gtf [fpkm, tpm]

source_name: Liver

extract_protocol: Livers were collected at necropsy and the left lateral lobe was used for RNA extraction. RNA extraction was performed using Qiagen’s RNeasy Mini Kit following the manufacturer’s protocol.

treatment_protocol: Wildtype or KDM1A transgenic male mice were fed either a low- or high-fat diet (10% or 60% kcal fat, respectively) for 10-12 weeks starting at weaning. All females used for breeding and all F1 and F2 were fed a regular chow diet.

value: Liver

value: 22 weeks

tag: genotype

value: Grandpaternal KDM1A transgenic

tag: diet

value: Grandpaternal high-fat diet

tag: Sex

value: male

tag: generation


title: EL4 GFP + GATA3 rep1


title: EL4 GFP + Plum rep1


title: DAUDI U2

source_name: BL cell line - DAUDI

growth_protocol: Cell lines were co-cultured with bone marrow stromal cells (BMSCs), M2-polarized macrophages and PBMCs (4:1:1:1) in the presence of 10 ng/mL TG-1801 +/- U2. After 24h incubation, CD20+ target cells were isolated using the EasySep Human Biotin Positive Selection Kit II (StemCell Technologies) and the biotinylated anti-CD20 antibody (BioLegend).

treatment_protocol: 10 ng/mL TG-1801 +/- U2 (10 µg/mL ublituximab + 1 µM umbralisib) for 24h

value: BL cell line

value: U2 combination


title: TGFb- stimulated NHDFs

city: Fukuoka

first: Hirohiko

last: Ise

address: Motooka 744

department: IMCE

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: NHDFs, TGFb-stimulated

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent introgen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: normal human dermal fibroblasts (NHDFs)

value: TGFb-stimulated


title: DAUDI COMBO

value: Triplet combination


title: f2_tg_hfd_male_RNA_rep2

tag: strain

tag: age


title: TGFb- stimulated NHDFs supplemented with cell debris from dead HeLa cells

source_name: NHDFs, TGFb-stimulated, supplemented with dead cell debris, 48 h.


title: TGFb- stimulated NHDFs supplemented with AC-GlcNAc10

source_name: NHDFs, TGFb-stimulated , supplemented with AC-GlcNAc10, 48 h.


title: IHT-IR rep2

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

data_processing:
Trimming of first 8bp using cutadapt
Mapped against hg38 genome using miARma-seq pipeline
Mapped BAM files were read into Qlucore to convert mapped data into expression values
FPKM normalization was used
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: BOECs

growth_protocol: Martin-Ramirez J, Hofman M, van den Biggelaar M, Hebbel RP, Voorberg J. Establishment of outgrowth endothelial cells from peripheral blood. Nat Protoc. 2012 Sep;7(9):1709-15. doi: 10.1038/nprot.2012.093. Epub 2012 Aug 23. PMID: 22918388.

extract_protocol:
RNeasy_ Mini kit (Qiagen)
QuantSeq 3´-mRNA Library Prep kit (Lexogen)
3' RNA-seq (Illumina HiSeq 2500 V4 platform)

treatment_protocol: No Treatment

tag: disease state

value: Healthy

tag: gender

value: Female


title: f2_crwt_hfd_male_RNA_rep4

value: Wildtype


title: IHT-IR rep1


title: IHT-AT rep2

value: type 3 von Willebrand disease


title: DAUDI Control

value: untreated


title: EL4 T-bet + Plum rep1

tag: cell line

value: FLAG-T-bet


title: Sarcoidosis patient 5 prior to treated with tofacitinib [SAR5_pr_pr]

city: New Haven

first: William

last: Damsky

address: 333 Cedar St

institute: Yale School of Medicine

description:
SAR5 pr
SAR5_pr_S25_L003

data_processing:
Reads were aligned using HISTAT2 (version 2.1.0) against the Genome Reference Consortium Human Build 38 (hg38)
Quantification was done using RefSeq Transcripts release 93.
Quantified reads were normalized to log2(FPKM+1
Differentially expressed genes between control, pre-treatment, and during treatment groups, was carried out on Qlucore Omics Explorer (version 3.5, Qlucore AB, Lund, Sweden)
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38
Supplementary_files_format_and_content: Normalized_counts_bulkrna.csv

source_name: Lesional skin

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini kits (Qiagen cat# 74704) according to the manufacturer’s instructions. Homogenization of the tissue was achieved using a rotor-homogenizer (PowerGen 125, ThermoFisher). .
RNA was submitted to the Yale Stem Cell Center and complementary DNA libraries were prepared and 100-base pair paired-end stranded sequencing was performed on an Illumina HiSeq 4000, also at Yale Stem Cell Center

treatment_protocol: Six patients with severe, long-standing sarcoidosis were enrolled and treated with tofacitinib monotherapy (5 mg twice daily) for 6 months. Concomitant methotrexate and/or low dose prednisone was allowed so long as the dose had been stable over the prior 3 months.

tag: subject status

value: Sarcoidosis patient

value: tofacitinib

value: skin


title: AC-GlcNAc10-treated NHDFs

source_name: NHDFs, treated with AC-GlcNAc10. 24 h

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (introgen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.


title: RAJI COMBO

source_name: BL cell line - RAJI


title: IHT-BP rep2

value: Male


title: EL4 GFP + GATA3 H3K27ac ChIP

data_processing:
Raw reads were ﬁltered for base quality using FastQC with default parameters and adapters sequences were removed with Trim Galore!
Reads passing quality filtering criteria were aligned to GRCm38 using BWA with default settings
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were lysed with non-ionic detergent, the nuclei washed and then lysed with ionic detergent. Cells were sonicated on ice to solubilize and shear crosslinked DNA (27W for 10x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell lysate was cleared by centrifugation and then incubated overnight at 4°C with 50 µl of Protein G magnetic Dynabeads that had been pre-incubated with 5 µg of purified antibody (anti-FLAG, M2 Sigma; anti-HA, 3F10 Roche; anti-H3K27ac, ab4729 Abcam). Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with rocking for 2 hrs and crosslinks then reversed in IP and input DNA by incubation at 65°C for 6 hrs. IP and input DNA were then purified by treatment with RNase A, proteinase K and isolated with KAPA Pure beads.
Libraries were constructed from ChIP DNA by standard Illumina protocols, except that DNA in the range 150-350 bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 50 bp single-end read sequencing with a HiSeq 2500 sequencer.

treatment_protocol: EL4 cells were stimulated with phorbol 12-myristate 13-acetate (50 ng/ml) and ionomycin (1 μM) for 4 hours prior to crosslinking. Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine as described. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen.

value: PMA  + inomomycin

tag: ectopically expressed protein

tag: antibody

value: anti-H3K27ac, ab4729 Abcam


title: IHT-AT rep1


title: f2_crwt_hfd_male_RNA_rep3

value: Liver

value: 22 weeks

value: Grandpaternal high-fat diet

value: male


title: f2_tg_hfd_male_RNA_rep1

value: Grandpaternal KDM1A transgenic


title: RAJI U2

value: BL cell line

value: U2 combination


title: IHT-BP rep1

value: Healthy


title: EL4 GFP + Plum H3K27ac ChIP


title: 42D-ENZR-shASCL1-ATAC

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

data_processing:
Base calling was performed using Bcl2fastq 2.17.1.14 with default parameters as per recommendation from Illumina.
Demultiplexing was also performed using Bcl2fastq 2.17.1.14 with default parameters as per recommendation from Illumina.
FastQC version 0.11.9 was used for quality control analysis of fastq files. Cutadapt v1.18 was used to trim adapter.
Raw reads were aligned to the hg38 (human) reference genome using BWA-MEM software (version 0.7.17) with default parameters. Alignments with mapping quality less than 60 were filtered out (leaving only uniquely mapped reads). Accessible DNA fragments datapoints were extracted using custom AWK script. The sam files were converted to bam files using Samtools software (version 1.1.2).
Narrow peaks were called using MACS2 callpeak (version 2.2.7.1) with options -f BAMPE -g 2.9e9 --keep-dup=1 -B -q 0.05 or -q 0.000001. Bedtools intersect (v2.28.0) program suite was used to generate shared (-wa -u -f 0.5 -F 0.5 -e) and unique (-v -f 0.5 -F 0.5 -e) peak set between samples.
Deeptools (v2.30.0) program suite was used to generate bigWig files.
HOMER (v4.11) program suite was used to annotate peaks and perform motif enrichment analysis.
Genome_build: hg38
Supplementary_files_format_and_content: NARROWPEAK (BED format)
Supplementary_files_format_and_content: bigWig

source_name: 42D Prostate cancer cell line generated from mouse xenograft of LNCaP

growth_protocol: 16D cells were cultured in RPMI-1640 media containing 5% fetal bovine serum, 42D ENZ-resistant (ENZR) cells were cultured in RPMI-1640 media containing 5% fetal bovine serum supplemented with 10mM ENZ, NCI-H660 cells were cultured HITES medium following ATCC recommendation.

extract_protocol:
Cell pellet of 50,000 cells per sample was used for library preparation. Genomic DNA fragments for ATAC seq library was prepared as per protocol published in Buenrostro et al. 2013 and Chen et al. 2018 with some modifications. Briefly, cells were collected by incubating in trypsin for 5 minutes at room temperature and subsequent centrifugation at 2300 rpm for 5 minutes at 4°C. Cells were washed twice and re-suspended in PBS. 5 x 104 cell pellet was used for tagmentation by incubating in 50 µl of 1x THS-seq buffer (25µl 2x THS-buffer, 5µl 10x Digitonin, 2µl Illumina-TDE1 (Cat FC-121-1030) or ActiveMotif-Tn5 (Cat 53150)) for 20 minutes at 37°C with 800 rpm in ThermoMixer (Eppendorf). To stop the tagmentation reaction, equal volume of 2x Tagmentation Stop Buffer [10mM Tris-HCl (pH 8.0), 20mM EDTA (pH 8.0)] was added to reaction and incubated for 10 minutes on ice. For cell lysis, equal volume of 2x Lysis Buffer [100 mM Tris-HCl (pH8.0), 100 mM NaCl, 40 µg/ml Proteinase K, 0.4% SDS] was added to the tagmentation mix and incubated at 65°C for 15 minutes. The tagmented DNA library was purified in 20 µl EB using Qiaquick PCR purification kit (Qiagen).
Library fragments were amplified using NEB Next High-Fidelity 2x PCR Master Mix (New England Biolab Cat #M0541) and custom Nextera PCR primers. Libraries were amplified for a total of 11 to 12 cycles and purified using Qiaquick PCR purification kit. Libraries were quantified by Qubit 1x dsDNA HS Assay kit (Cat Q33230), quality assessed by Agilent Bioanalyzer run using Agilent High Sensitivity Assay (kit no. 5067-4626) and sequenced using 75bp or 125bp Paired-end sequencing on a Illumina HiSeq 2500 following manufacturer's protocol.

treatment_protocol: 16D cells in RPMI-1640 media containing 5% fetal bovine serum were treated with 10mM ENZ for 3 or 10 days. First, ASCL1 was knock down using short-hairpin (sh) RNA strategy in 42D-ENZR to generate 42D-ENZR-shASCL1 cell line before being used for ATAC seq sample preparation.

value: ENZ-resistant CRPC-NE

value: Enzalutamide

value: AR positive, Neuro Endocrine like

tag: shRNA


title: EL4 T-bet + GATA3 H3K27ac ChIP

value: FLAG-T-bet + HA-GATA3


title: EL4 T-bet + GATA3 rep1


title: RAJI Control

value: untreated


title: f2_crwt_hfd_male_RNA_rep2

value: Wildtype


title: f2_crwt_hfd_male_RNA_rep1


title: EL4 T-bet + GATA3 FLAG-T-bet ChIP rep2

value: anti-FLAG, M2 Sigma


title: DAUDI 1801


title: EL4 T-bet + Plum HA-GATA3 ChIP rep2

value: PMA  + inomomycin

value: anti-HA, 3F10 Roche


title: NCI-H660-ATAC

source_name: Cell line generated from patient (ATCC CRL-5813)

value: Neuro Endocrine Prostate Cancer

value: AR negative, Neuro Endocrine


title: EL4 T-bet + Plum FLAG-T-bet ChIP rep2

value: FLAG-T-bet


title: EL4 T-bet + Plum H3K27ac ChIP

value: anti-H3K27ac, ab4729 Abcam


title: hippocampal microglia sample 72

city: Rochester

first: O'Banion

last: Kerry

state: United States of America

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Basecalls: bcl2fastq-2.19.0
Data Cleaning: fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment: STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification: subread-1.6.4, featurecounts, -s 0 -t exon -g gene_name
Genome_build: Reference Genome: GRCm38.p6 + Gencode-M22 Annotation
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampal microglia

extract_protocol:
Microglia (CD45int CD11b+) were sorted with FACSAria II (BD) into RLT Buffer (Qiagen).
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) and pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA).

treatment_protocol: Gas6(Myc-DDK-tagged)-mouse growth arrest specific 6 (Gas6) cDNA was purchased from OriGene (Catalog #, Rockville, MD) and used to construct an AAV-packaging vector using In-Fusion HD Cloning Kit (Catalog #, Clontech Laboratories). The cloning vector was packaged into AAV-1 under the SYN1 promoter at the National Institute of Drug Abuse at the NIH by Brandon Harvey. A deletion mutant lacking the Gas6 Gla and EGF domains was created and processed as above. A 33 GA needle was lowered into the burr hole (1.8mm caudal, +/- 1.8mm lateral to bregma) and 1.5ul of AAV-Gas6 or AAV-Gas6(delta)(1E12 vg/ml) was injected over 10 minutes.

value: APP

value: Control

value: F


title: AA1912 1801

source_name: BL primary cells (patient AA1912)

growth_protocol: Primary samples were co-cultured with bone marrow stromal cells (BMSCs), M2-polarized macrophages and PBMCs (4:1:1:1) in the presence of 10 ng/mL TG-1801 +/- U2. After 24h incubation, CD20+ target cells were isolated using the EasySep Human Biotin Positive Selection Kit II (StemCell Technologies) and the biotinylated anti-CD20 antibody (BioLegend).

value: primary BL cells from patient


title: AA1912 COMBO

value: Triplet combination


title: AA1912 U2

value: U2 combination


title: 16D-CRPC-3d-ENZ-ATAC

source_name: 16D Prostate cancer cell line generated from mouse xenograft of LNCaP

value: Castration Resistant Prostate Cancer (CRPC)

value: Enzalutamide

tag: time point

value: Castration resistant


title: EL4 GFP + GATA3 HA-GATA3 ChIP rep2


title: hippocampal microglia sample 59


title: hippocampal microglia sample 70


title: RAJI 1801

tag: cell type

value: BL cell line


title: 16D-CRPC-10d-ENZ-ATAC


title: EL4 T-bet + GATA3 FLAG-T-bet ChIP rep1

value: FLAG-T-bet + HA-GATA3

value: anti-FLAG, M2 Sigma


title: 16D-CRPC-0d-ENZ-ATAC


title: hippocampal microglia sample 57

value: NTg


title: NHDF (Control)ｶｲｾk

source_name: NHDFs

value: normal human dermal fibroblasts (NHDFs)


title: AA2000 COMBO

source_name: BL primary cells (patient AA2000)


title: hippocampal microglia sample 48


title: hippocampal microglia sample 76


title: EL4 T-bet + Plum FLAG-T-bet ChIP rep1

source_name: EL4 cell line

value: PMA  + inomomycin


title: CaSki-4 RNA-seq

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Basecalling was performed using RTA version 2.4.11
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 1.8.4) allowing 1 mismatch.
Trimming of adapters and low-quality bases was performed using CutAdapt (v.1.16).
Mapping to the hybrid genome containing hg38 and HPV16 or HPV18 was performed using STAR 2.5.2b
The following parameters were used: "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --readFilesCommand zcat --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing output of STAR Chimeric.out.junction

source_name: CaSki cell

growth_protocol: All cell lines were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum (FBS, GE Healthcare, Logan, UT) at 37°C under a 5% CO2 atmosphere.

extract_protocol:
The total RNA was isolated using TriPure Reagent (Millipore-Sigma, Part No. 11667165001)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CaSki

value: female

tag: cancer type

value: Cervical


title: 42D-ENZR-ATAC

value: ENZ-resistant CRPC-NE

tag: treatment

value: AR positive, Neuro Endocrine like


title: AA1912 Control

value: primary BL cells from patient

value: untreated


title: EL4 T-bet + Plum HA-GATA3 ChIP rep1

value: anti-HA, 3F10 Roche


title: EL4 GFP + GATA3 HA-GATA3 ChIP rep1


title: AA2000 U2

value: U2 combination


title: AA2000 1801


title: CaSki-2 RNA-seq


title: 41_HC_KO

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

data_processing:
Low quality reads and and contaminants (e.g. sequence adapters) were removed using Trimmomatic (version 0.32)
Sequences were aligned to the GRCm38  genome using HiSat2 (version 2.1.0)
Transcript abundance level (Transcript count) was generated using HTSeq (version 0.9.1)
The transcript counts were further processed using R software environment for statistical computing and graphics (version 3.4.0)
Differential expression was performed using edgeR R package using the negative binomial GLM approach
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files containing read counts per gene

source_name: Hepatocytes

growth_protocol: Mice were housed under standard conditions with ad libitium access to water and chow. Mice were euthanized, the liver was isolated, digested and different liver cell types were isolated using density centrifugation/FACS, collected in lysis buffer and lysates were stored at -80ºC.

extract_protocol:
RNA was extracted using Reliaprep (Promega) according to manurfacturer's protocol.
Illumina TruSeq stranded mRNA Library prep kit and resulting cDNA libraries were sequenced according to the Illumina TruSeq Rapid v2 protocol on an Illumina HiSeq2500 sequencer

treatment_protocol: Mice expressing floxed alleles of Zeb2 with endothelial cell-specific Cre expression were treated with tamoxifen (2mg/day for 5 consecutive days) to delete Zeb2 in endotheilal cells; tamoxifen-treated littermates not expressing Cre were used as wild-type controls.

tag: genotype

value: endothelial-specific Zeb2 knock-out

tag: developmental stage

value: adult

tag: tissue

value: unchallenged liver

value: Hepatocytes


title: 25_HC_KO


title: CaSki-1 RNA-seq


title: B3

city: beijing

first: jing

last: hang

address: No.49 huayuan north road

country: China

institute: peking university, third hospital

data_processing:
NGSQC was used for adaptor-moving and quality control filtration
reads were mapped to genome by HISAT2 v2.1.0 and estimated with online Picard
fragment counts normalized per kilobase of exon per million mapped fragments (FPKM) was estimated using cufflink
classification of AS and evaluation of differentially alternative spliced genes were analyzed using Rmats and Asprofile
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 6 samples output from cufflink
Supplementary_files_format_and_content: tab-delimited text files include JC statistics for 6 samples output from rMATS

source_name: oocyte

extract_protocol:
PicoPure RNA Extraction kit (Life Technologies) and CWBIO Gel Extraction Kit (Cwbiotech, Inc.) were used to for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: health status

value: in vivo matured


title: AA2000 Control


title: B2


title: 33_HC_WT

value: wild-type


title: hippocampal microglia sample 25

value: NTg

tag: Sex

value: M


title: D283MED cell lines conditionally expressing KBTBD4 R311PR,  doxycycline treated, Replicate 4

city: Oxford

first: Vincenzo

last: D'Angiolella

state: Oxfordshire

address: Old Road Campus Research Building, Old Road Campus, Off, Roosevelt Dr

institute: University of Oxford

data_processing:
basecallling: Illumina CASAVA
mapping to reference : HISAT2 v2.0.5
transcript assembly :  StringTie v1.3.1
QC: removing reads containing adapter and poly-N sequences and reads with low quality from raw data
Raw gene-level count generation: StringTie v1.3.1
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: D283Med cells were grow in MEM supplemented with 10% FBS (tetracycline-free)

extract_protocol: After washed once in phosphate-buffered saline, cell pellet was resuspended in TRIzol Reagent (Thermo Fisher Scientific cat # 15596026) and extracted following the manufacturer's protocol.

treatment_protocol: Cells were treated with 1ug/ml of doxycycline for 4 days

value: doxycycline, 1ug/ml for 4 days

value: D283Med - medulloblastoma cell line


title: hippocampal microglia sample 19

value: APP


title: D283MED cell lines conditionally expressing KBTBD4 R311PR,  doxycycline treated, Replicate 3


title: Y3

value: maturation deficient


title: hippocampal microglia sample 42

value: Control

value: F


title: hippocampal microglia sample 17


title: 32_SC_WT

source_name: Hepatic stellate cells

value: Hepatic stellate cells


title: Y2


title: B1


title: D283MED cell lines conditionally expressing KBTBD4 R311PR,  doxycycline treated, Replicate 2


title: 40_SC_WT


title: hippocampal microglia sample 26


title: D283MED cell lines conditionally expressing KBTBD4 R311PR,  doxycycline treated, Replicate 1


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR,  doxycycline treated, Replicate 4


title: hippocampal microglia sample 27


title: hippocampal microglia sample 11


title: 20_SC_KO


title: hippocampal microglia sample 15


title: hippocampal microglia sample 33


title: CaSki-3 RNA-seq

value: CaSki

value: female

value: Cervical


title: 43_KC_KO

source_name: Kupffer cells

value: endothelial-specific Zeb2 knock-out

value: adult

value: Kupffer cells


title: hippocampal microglia sample 16


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR,  doxycycline treated, Replicate 3


title: hippocampal microglia sample 9


title: hippocampal microglia sample 8


title: 29_HC_WT

value: unchallenged liver

value: Hepatocytes


title: D283MED cell lines conditionally expressing KBTBD4 WT,  doxycycline treated, Replicate 3


title: hippocampal microglia sample 10

value: NTg


title: 0730.C2

first: Lauro

last: Sumoy

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

description:
small RNAsequencing analysis
JManyeDE_report.xlsx

data_processing:
BCL basecall files were converted to FASTQ per sample using CASAVA v1.8.2 (Illumina) with default parameters to generate demultiplexed per sample fastq raw sequencing data files.
Per sample read quality was assessed using the fastx_quality stats software (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
A filtering step was introduced to leave out miRNAs detected at very low levels -i.e. absent in a fraction of samples- which were not considered in statistical analysis.  Analysis was only done at the mature miRNA level.
Statistically significant differences in miRNA expression were determined both by EdgeR and DESeq2 (Love, 2014) with multiple testing adjustment.
Genome_build: Reads were mapped to the human genome hg19 assembly (UCSC) and assigned to different RNA collections based on ENSEMBL annotation.
Supplementary_files_format_and_content: Processed miRNA expression profiling (miRNA identifiers based on miRBase 20) data tables are provided as a supplementary file in excel workbook (.xlsx) format. It includes 6 worksheets named 'RawCounts' (table of summarized read counts for each miRNA in every sample), 'NormDESeq2'  and 'NormEdgeR'  (normalized read counts for all samples derived from the two programs used, DESeq2 and egdeR respectively), 'rLog' (rLog transformed normalized counts used as input for clustering and visualization by DESeq2), 'diffExp' and 'diffExp_sin_285-C1' (differential expression results from all samples and excluding one outlier sample); each table includes separate sets of columns for each comparison with the default output from edgeR (logFC, logCPM, PValue, FDR) and DESeq2 (baseMean, log2FoldChange, lfcSE, stat, pvalue, padj) for all comparisons. Column headers: logFC or log2FoldChange (log2 fold changes), average abundance measure (logCPM -average log counts per million from edgeR-, baseMean -average normalized counts from DESeq2-), nominal p value (PValue, pvalue), adjusted p value (FDR -false discovery rate from edgeR-, padj -adjusted pvalue by default Benjamini and Hochberg method from DESeq2-), and statistics (lfcSE -log fold change standard error-, stat -Wald-test statistic- both measures as determined by DESeq2).

source_name: plasma

extract_protocol:
Blood samples were collected in EDTA tubes, then, plasma samples were obtained by a single centrifugation (1000g, 15min. at room temperature). For RNA extraction from 200ul of plasma, miRCURY RNA insolation kit-Biofluids (#300112) was used following manufacturer indications with modifications that included using glycoingen as carrier and a 1:50 dilution of spike in RNA.
Barcoded sequencing libraries were prepared using the TrueSeq SmallRNA library kit (Illumina) with slight modifications from the default recommendations (Part # 15004197 Rev. F, February 2014). Modifications included using all RNA extracted from 200 ul of plasma, in the subnanogram range, and increasing the number of cycles in the final PCR reaction (from 12 to 15).
Libraries were quality assessed with Bioanalyzer DNA 1000 assays (Agilent). Bioanalyzer concentration estimates were used to generate an equimolar library mix. The library pool was automatically size selected (135-160bp) using 3% agarose dye free cassettes with 3% DF marker F on a Pippin Prep system with software v.6.0 (Sage Science). QIAquick (Qiagen) column purifications were performed prior and after to size selection. The library pool was quantifiedby PCR with theKAPA Library Quantification Kit following manufacturer’s instructions (Roche). The library pool was run on 4 lanes of 1x50 bp sequencing was performed on HiSeq2500 platform (Illumina) using adapted protocols for TruSeq SR cluster kit v3 (Part#15023335) following cBot™ (Part#15006165) and HiSeq2500 System (Part#15035786) user guidelines. Raw data were analysed by Real Time Analysis software v. 1.17.21.3 and Sequence Analysis Viewer software v. 1.8.20 (Illumina.).

value: UC

tag: corticosteroid response

value: Glucocorticoid non-responder

tag: collection time

value: 3rd day after starting Glucocorticoid treatment

tag: age (years)

value: Female

tag: individual

tag: sample type

value: plasma


title: 1193.C2

tag: disease state

value: Male


title: 8_SC_KO


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR,  doxycycline treated, Replicate 2

value: doxycycline, 1ug/ml for 4 days

value: D283Med - medulloblastoma cell line


title: D283MED cell lines conditionally expressing KBTBD4 WT,  doxycycline treated, Replicate 4


title: 1416.C2


title: 1238.C2


title: Y1

value: maturation deficient


title: 46_EC_KO

source_name: Endothelial cells from liver

value: Endothelial cells from liver


title: 39_KC_WT

value: wild-type


title: hippocampal microglia sample 7

value: Control

value: M


title: 27_KC_KO

value: endothelial-specific Zeb2 knock-out

value: adult

value: Kupffer cells


title: D283MED cell lines conditionally expressing KBTBD4 WT,  doxycycline treated, Replicate 2


title: hippocampal microglia sample 6

value: APP


title: 31_KC_WT

value: unchallenged liver


title: 0577.C2

value: UC

value: Glucocorticoid non-responder


title: 6_EC_KO


title: hippocampal microglia sample 5


title: D283MED cell lines conditionally expressing KBTBD4 R311PR - Replicate 4

value: no treatment


title: hippocampal microglia sample 3

value: NTg

value: F


title: 1106.C2

value: 3rd day after starting Glucocorticoid treatment

value: Female

value: plasma


title: hippocampal microglia sample 2


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR,  doxycycline treated, Replicate 1

value: doxycycline, 1ug/ml for 4 days

value: D283Med - medulloblastoma cell line


title: 0462.C2

value: Male


title: D283MED cell lines conditionally expressing KBTBD4 WT,  doxycycline treated, Replicate 1


title: 1213C2


title: D283MED cell lines conditionally expressing KBTBD4 R311PR - Replicate 1


title: 1279.C2


title: D283MED cell lines conditionally expressing KBTBD4 R311PR - Replicate 2


title: hippocampal microglia sample 4


title: 34_EC_WT

value: wild-type

value: Endothelial cells from liver


title: 38_EC_WT

value: adult


title: 0714.C2


title: D283MED cell lines conditionally expressing KBTBD4 R313PRR - Replicate 4


title: input_ESC_dTAG_24h_Med23

city: Berlin

first: Sara

last: Hetzel

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

description: ChIP sequencing of mESCs

data_processing:
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC). Reads were aligned separately to the mouse genome (mm10) and to the fly genome (D. Melanogaster, dm6) using bwa with the 'mem' command (version 0.7.17, default parameters). A sorted BAM file was obtained and indexed using samtools with the 'sort' and 'index' commands (version 1.10). Duplicate reads were identified and removed using gatk (version 4.1.4.1) with the 'MarkDuplicates' command and default parameters. Technical replicates of treatment and input samples were merged respectively using samtools 'merge'.
Peaks were called with reads aligning to the mouse genome only using MACS2 'callpeak' (version 2.1.2; parameters --bdg --SPMR) using the input samples as control samples. For H3K9me3 only, the '--broad' option was used. Genome-wide coverage tracks for single and merged replicates normalized by library size were computed using bamCoverage (version: 3.4.3; parameters: --normalizeUsing CPM --extendReads) and in addition normalized by the spike-in factor obtained from the reads aligning to the drosophila genome.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig coverage files
Raw reads of treatment and input samples were subjected to adapter and quality trimming with cutadapt (version 2.4; parameters: --nextseq-trim 20 --overlap 5 --minimum-length 25 --adapter AGATCGGAAGAGC -A AGATCGGAAGAGC). Reads were aligned to the mouse genome (mm10) using bwa with the 'mem' command (version 0.7.17, default parameters). A sorted BAM file was obtained and indexed using samtools with the 'sort' and 'index' commands (version 1.10). Duplicate reads were identified and removed using gatk (version 4.1.4.1) with the 'MarkDuplicates' command and default parameters. Technical replicates of treatment and input samples were merged respectively using samtools 'merge'.
Peaks were called with reads aligning to the mouse genome using MACS2 'callpeak' (version 2.1.2; parameters --bdg --SPMR) using the input samples as control samples. Genome-wide coverage tracks for single and merged replicates normalized by library size were computed using bamCoverage (version: 3.4.3; parameters: --normalizeUsing CPM --extendReads).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig coverage files

source_name: mESC

growth_protocol: During expansions, cells were cultured on irradiated primary mouse embryonic fibroblasts (MEFs) under serum/LIF conditions: knockout DMEM containing 15 % fetal bovine serum,  50 µg/ml penicillin/streptomycin, 2 mM L-Glutamine, 100 µM non-essential amino acids, 80 µM ß-mercaptoethanol and 1000 U/ml LIF. Before starting ChIP-Seq experiments, mESCs were depleted from MEFs by incubating them on gelatin coated cell culture plates for 45 min in +37 C allowing MEFs to attach while mESCs remain in suspension. MEF depletion was performed two times after which mESCs were seeded on gelatin coated plates and maintained in serum/LIF conditions with 2000 U/ml LIF.

extract_protocol:
Cells were detached with TrypLE, washed once with PBS, and protein-protein crosslinking was performed by incubating cells in rotation with 2 mM disuccimidyl glutarate in PBS for 45 min in room temperature. Cells were washed twice with PBS and DNA-protein crosslinking was performed with 1 % formaldehyde for 10 minutes in room temperature followed by quenching with 125 mM glycine. For each sample, ten million mESCs were lysed in LB1 (50 mM HEPES-KOH, 140 nM NaCl, 1 mM EDTA, 10 % glycerol, 0.5 % Igepal ca-630 and 0.25 % Triton X-100, 5 mM Na-butyrate and 1x protease inhibitor cocktail) and collected by sentrifugation. Lysis was continued in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 5 mM Na-butarate and 1 x protease inhibitor cocktail) followed by sentrifugation, nuclei were lysed in sonication buffer (50 mM HEPES-KOH pH 7.5, 140 mM EDTA, 1 mM EDTA, 1 mM EGTA, 1 % Triton X-100, 0.1 % Na-deoxycholate, 0.1 % SDS and 1x protease inhibitors (Roche)) and sonicated for 50 cycles by using Bioruptor NextGen (high setting). Ten percent of sample material was set aside as input and stored in +4C. Voume was adjusted to 200 µl with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS) and crosslinks were reversed by incubating samples in 65C for 16 hours. Samples were topped up with 200 µl TE buffer and 8 µl of RNAse A, incubated in 37 C for 2 hours followed by addition of 7 µl of 300 mM CaCl2, 2 µl Proteinase K (Ambion) and 30 minutes incubation in 37C. DNA purified from samples with phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation.
10 ng of DNA was used to prepare sequencing libraries with KAPA HyperPrep Kit (Roche) according to manufacturer's instructions.

tag: strain

value: dTAG