title: PS43

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: not included in the analysis

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. F1- F3 generation control and  pesticides lineages were housed in the same room and racks with lighting, food and water. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).

extract_protocol:
For each sample, the epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm.  The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing.   DNA protocol: While sperm are thawing, turn on the centrifuge to 4ºC.   1. Re-suspend sperm pellet with pestle (and pestle motor if available).   o If there is some liquid left with the pellet, there is no need to add any additional buffer  o If not add 100 µL 1xPBS or NIM buffer  2. Take 25 to 50 µL of the suspension (depending on how big the pellet is) and transfer it to a microfuge tube with 200 µL 1xPBS.   o Mix  3. Sonicate suspension at 25% with probe sonicator for 5 seconds.  4. Spin at 12,000 rpm for 10 minutes at 4˚C.  o While waiting, turn on heat plate to 65˚C   5. Discard supernatant. Be careful – pellet is loose.  6. Wash with 200 µL 1xPBS and spin as above.  o While waiting, retrieve DTT from freezer (make sure there is enough)    o Turn on the incubator  o Vortex DTT once it has thawed a bit  7. Resuspend pellet in 100 µL 1xPBS, then continue with protocol below.  General:  1. Re-suspend tissue in 100 µL PBS or NIM buffer, then   o add 820 µL DNA extraction buffer   o add 50 µL 0.1M DTT   o vortex briefly  o incubate at 65˚C for 15 minutes   o Retrieve ProteinaseK from freezer  2. Add 50 µL proteinase K (20 mg/ml) and   o incubate at 55˚C for 2-3 hours under constant rotation  o use Eppendorf SafeLock tubes and wrap the tops with Parafilm  3. After incubation add 300 µL of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A)  o mix (vortex) thoroughly and make sure that the solutions are mixed   o then incubate for 20 min on ice (or longer if needed)  4. Centrifuge at 13,500 g for 30 minutes at 4˚C.  o Prepare 2 mL tubes  o Take glycoblue out of the freezer  5. Transfer 1 ml of the supernatant to a new 2 ml tube.   o add 2 µL of glycoblue   o add 1 ml of cold 100 % isopropanol  6. Mix well by inverting tubes several times.  7. Incubate for 60 min at -20˚C.  8. Centrifuge for 20 min at 13,500 g at 4˚C.   9. Take off and discard supernatant without disturbing (blue) pellet.   10. Wash pellet 2-3 times with 70% cold ethanol.   o Add 500µL of 70% ethanol to each pellet and   o return to freezer for 20 minutes  11. Centrifuge for 10 min at 4˚C at maximum speed (18,200 g)   o discard supernatant  12. Spin again briefly to collect residual ethanol at bottom of tube and remove as much liquid as possible with gel loading tip.  13. Air-dry at RT until pellet looks dry, but be careful not to over-dry.   o This will take about 5 minutes  14. Re-suspend in 100 µL of nuclease free water or TE.  15. Measure DNA concentration using Nanodrop.   Methylated DNA immunoprecipitation protocol: Shear & Add Antibody to DNA  1. Sonicate purified genomic DNA using Covaris:  a. Dilute 6μg genomic DNA into 50 or 130 μl TE buffer in the appropriate Covaris tube.  b. Set Covaris to desired program (300 or 500 bp program works well).  c. Run program for each tube  • While waiting, turn on the dry bath to 95ºC.   2. Run 10 μl sonicated DNA & 5 μl DNA ladder on 2% agarose gel to verify fragment size.  • While waiting for gel, clean up Covaris.   3. Measure volume of sonicated DNA after gel run.  4. Dilute sonicated DNA with TE buffer to 400 μl (400 – 130 + 10 = 280 µL)  5. Heat-denature for 10min at 95˚C, and   • immediately cool on (watery) ice for 5min  6. To the denatured sonicated DNA:  a. Add 100μl of cold 5X IP buffer   b. Add 5μg (volume depending on concentration) of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006). ALWAYS check antibody concentration. Diagenode sometimes changes it.  c. Incubate the DNA-antibody mixture overnight on a rotator at 4˚C.  Rotate at a low enough speed to prevent significant foaming.  Bind Beads to DNA: Antibody Mixture  1. Pre-wash Magnetic Beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) as follows:  • Resuspend the beads in the vial (pipet up and down or rotate, do not vortex)  • Transfer desired volume (50 μl per sample) to a centrifuge tube, add the same volume of Washing Buffer (at least 1 mL), and resuspend.  • Place the tube in a magnet for 1-2 minutes and discard supernatant.   • Resuspend beads in 1 ml of washing buffer and incubate for 1 minute on bench. Put tube on magnet for 1-2 minutes and discard supernatant.  • Remove the tube from the magnet and resuspend the washed beads in the same volume of 1xIP buffer as the initial volume of beads.  2. Add 50μl of beads to the 500μl of DNA-antibody mixture from step 2  3. Incubate 2h on a rotating platform at 4˚C.  Wash DNA: Antibody: Beads Mixture & Add Proteinase K Mix  1. Wash beads three times with 1X IP buffer as follows:  • Place tube in magnet for 1-2 minutes and discard supernatant  • Remove tube from magnet  • Add 1ml cold 1X IP buffer  • Mix by inverting tube or gently vortexing (set Vortex to low).  • Incubate tube(s) for 1 minute on bench.  • Place tube in magnet for 1-2 minutes and discard supernatant  • Repeat twice for a total of 3 washes  2. Resuspend the beads in 250μl digestion buffer.  3. Add 3.5μl Proteinase K Mix (20mg/ml) to the resuspended beads.  4. Incubate 2-3 hours on a rotating platform at 55˚C (make sure to seal lids so they don’t leak). Use USA Scientific SealRite tubes or Eppendorf Safe-Lock tubes and seal top with Parafilm.  Purify DNA  • Retrieve Glycoblue from freezer.   1. Remove Parafilm and add 250μl Phenol-Chloroform-Isoamylalcohol to each tube.    • Vortex for 30 sec and centrifuge at 14,000g for 5min at RT.  • Remove the aqueous supernatant and transfer to a fresh microcentrifuge tube.  2. Add 250μl chloroform to the supernatant from step 1.    • Vortex for 30sec and centrifuge at 14,000g for 5min at RT.   • Remove the aqueous supernatant and transfer to a fresh microcentrifuge tube.  3. Add 500 μl ethanol  • Then add 20μl 5M NaCl   • Then add 2μl glyco-blue (20mg/ml)   • Vortex well   4. Precipitate in -20˚C freezer for 1 hour to overnight.  5. Centrifuge at 14,000g for 20min at 4˚C.  Carefully remove the supernatant, while not disturbing the pellet.  6. Wash the pellet with 500μl cold 75% ethanol. Leave in -20˚C freezer for 15 min.  7. Centrifuge at 14,000g for 5min at 4˚C.  Carefully remove the supernatant.  8. Completely dry samples.  9. Resuspend in 25μl H2O.    10. Measure the DNA concentration in Qubit with ssDNA kit and matching buffer.
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra DNA Library following the manufacturer’s protocol  and indexing each sample individually with NEBNext Multiplex Oligos for Illumina. NEBNext Ultra II Library Prep Kit for Illumina: ssDNA  • Start with 20 µl in PCR strips.   o ~40 ng of DNA  o Complete the volume to 20 µl   • Add 2.5 µL of diluted (1:10) random primer to each tube.   o for 10 samples, 27 µL 0.1x TE and 3 µL primers  o for 12 samples 36 µL 0.1x TE and 4 µL primers  o for 22 samples, 54 µL 0.1x TE and 6 µL primers  • Place strips in the thermocycler and use the Denaturation program. Immediately remove (as soon as time runs out on the program) and cool on watery ice following denaturation. Let tubes rest on watery ice for 5 minutes, then transfer to refrigerated block.   I. Second Strand cDNA Synthesis  Assemble the second strand cDNA synthesis reaction on ice by adding the following components to the 20 µl DNA.   Second Strand Synthesis Reaction  DNA          20 µL  ORANGE NEBNet 2nd Strand Synthesis Reaction Buffer  8 µL  ORANGE NEBNext 2nd Strand Synthesis Enzyme Mix 4 µL  Nuclease-free water      45.5 µL  Total Volume

treatment_protocol: Outbred Sprague Dawley gestating female rats (F0 generation) were administered an intraperitoneal dose of permethrin (150 mg/kg bodyweight/day) and DEET (40 mg/kg bodyweight/day). These doses were administered at 90 days of age, during embryonic days 8-14 (E8-E14) of fetal gonadal sex determination. The F1 generation offspring was directly exposed as a fetus and F2 generation grand-offspring exposed as the germline in the F1 generation. These were each bred at 90 days of age within the lineage. The F3 generation great-grand-offspring is required to establish the transgenerational inheritance generation of ancestral exposure.

tag: generation

value: 1 year

value: Sperm

tag: measurement

value: MeDIP

tag: disease

tag: lineage

value: pesticides


title: Lef1-CUT&RUN activated Treg rep1

status: Public on Nov 12 2020

type: SRA

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

country: China

institute: SJTU

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align ChIP-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ChIP-seq duplicates: Picard v1.141
Call ChIP-seq peaks: MACS2 v2.1.1
Align CUT&RUN reads: STAR v2.5.0c [disable splicing alignment]
Remove CUT&RUN duplicates: Picard v1.141
Call CUT&RUN peaks: MACS2 v2.1.1
Genome_build: GRCm38 and CAST/EiJ
Supplementary_files_format_and_content: raw read count

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Antibody targeted pA/G-MNase cleavage followed by Qiagen MinElute reaction cleanup
Kapa hyper prep kit

tag: strain

value: B6/Cast F1

tag: genotype

tag: cell type

value: CD44+CD62L- Foxp3+ CD4 T cells


title: TM22E-Dot1Li-PLX-Neg

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Boulevard

country: USA

institute: University of Pennsylvania

description:
processed data file:
WM989_timeMachineSort_Dot1Li_TPMdata.csv
meltedData_TM22E.tsv

library_source: transcriptomic

data_processing:
bcl2fastq conversion performed on BaseSpace using Illumina's default generate fastq workflow
Aligned to hg19 using STAR version 2.5.2a with default parameters
Filtered uniquely mapped reads using ngsutils/bamutils
Sorted using samtools-0.1.19
enumerated read counts per gene using HTseq-0.6.1 in union mode
normalized by sequencing depth and gene length using custom R script
Genome_build: aligned to hg19, ensembl GRCh37.75 gtf used for gene annotations
Supplementary_files_format_and_content: tsv files contain gene level RNA-seq counts generated using HTSeq with GRCh37.75 gene annotations. csv files contain RPM, RPKM, and TPM normalized counts as well as basic gene annotations (e.g. protein-coding, etc, lincRNA, rRNA etc.).

molecule: polyA RNA

organism: Homo sapiens

source_name: WM989 A6-G3 melanoma

growth_protocol: Grown in TU2% media

extract_protocol:
RNA extracted using Macharey-Nagel Nucleospin total RNA FFPE XS kit
NEBNext single cell/low input RNA library prep kit for illumina
mRNA-seq, poly-dT primed RT, unstranded.

treatment_protocol: When indicated, treated with 4 micromolar pinometostat or equal concentration DMSO for 5 days (replacing media with drug on day 3). When indicated, treated with 1 micromolar PLX4032 for 3 weeks (replacing media with drug every ~ 3 days).

tag: cell line

value: clonal melanoma cell line

tag: clone id

tag: treatment

value: 4 micromolar pinometostat for 5 days then 1 micromolar PLX4032 for 3 weeks

tag: experiment name (replicate)

tag: technical replicate


title: PS42

description: not included in the analysis

organism: Rattus norvegicus

tag: age


title: PS40

description: prostate.dmr.results.csv.gz

value: prostate disease


title: PS41

description: kidney.dmr.results.csv.gz

value: kidney disease


title: TM22E-Dot1Li-PLX-A647


title: Sample S2 technical replicate c

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Saline rat 2 technical replicate c

data_processing:
Illumina bcl2fastq 2.17.1.14 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 2.0-beta4. Before mapping, reads ≤40 bases were removed, and reads with  quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (rnor6 genome assembly from Ensembl version 84) using the STAR mapper (version 2.4.0k, with --outSAMunmapped Within parameter). Alignments from reads matching more than once on the genome were removed. Rattus norvegicus GFF3 genome annotation from from Ensembl version 84 was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted with HTSeq-count 0.5.3.
Genome_build: rnor6 version Ensembl 84
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

molecule: total RNA

source_name: Nucleus accumbens

extract_protocol:
Total RNA was extracted from bilateral nucleus accumbens and caudate putamen with RNeasy Qiagen mini kit according to the lipid tissue protocol of the manufacturer (Qiagen, Courtaboeuf, France)
Messenger (polyA+) RNAs were purified from 500 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina)

tag: genetic background

value: Sprague-Dawley

tag: phenotype

value: Saline Rat

value: 15 physiological serum injections


title: PS36

description: multiple.dmr.results.csv.gz

value: multiple disease


title: PS39

description: not included in the analysis

value: tumor


title: Lef1-CUT&RUN resting Treg rep1

value: CD44-CD62L+ Foxp3+ CD4 T cells


title: TM22E-Dot1Li-PLX-A546


title: PS37

description: multiple.dmr.results.csv.gz


title: PS38

description: multiple.dmr.results.csv.gz


title: TM22E-Dot1Li-CC-Neg-2

value: 4 micromolar pinometostat for 5 days


title: TCF1-CUT&RUN (exp2) activated Tcon rep2

value: CD44+CD62L- Foxp3- CD4 T cells


title: TM27-DMSO-CC-Dependent

description:
processed data file:
WM989_timeMachineSort_Dot1Li_TPMdata.csv
meltedData_TM27.tsv

value: DMSO 5 days


title: PS34

description: multiple.dmr.results.csv.gz

value: 1 year

value: Sperm

value: MeDIP


title: PS33

description: not included in the analysis

value: late puberty

value: pesticides


title: PS35

description: multiple.dmr.results.csv.gz


title: TCF1-CUT&RUN (exp2) activated Tcon rep1

value: B6/Cast F1


title: TM22E-Dot1Li-CC-Neg-1

value: clonal melanoma cell line


title: TM22E-Dot1Li-CC-A647-2


title: PS31

description: kidney.dmr.results.csv.gz

value: kidney disease


title: TM22E-Dot1Li-CC-A647-1


title: PS29

description: multiple.dmr.results.csv.gz


title: TCF1-CUT&RUN (exp2) resting Tcon rep2

value: CD44-CD62L+ Foxp3- CD4 T cells


title: PS28

description: kidney.dmr.results.csv.gz


title: TCF1-CUT&RUN (exp2) resting Tcon rep1


title: TM22E-Dot1Li-CC-A546


title: Lef1-CUT&RUN resting Treg rep2


title: TCF1-CUT&RUN (exp2) activated Treg rep2

value: CD44+CD62L- Foxp3+ CD4 T cells


title: PS26

description: prostate.dmr.results.csv.gz

value: prostate disease


title: PS25

description: kidney.dmr.results.csv.gz


title: TM22E-DMSO-PLX-Neg

value: DMSO 5 days then 1 micromolar PLX4032 for 3 weeks


title: TCF1-CUT&RUN (exp2) activated Treg rep1


title: TCF1-CUT&RUN (exp2) resting Treg rep2


title: PS22

description: multiple.dmr.results.csv.gz

value: multiple disease


title: PS23

description: kidney.dmr.results.csv.gz


title: PS32

description: multiple.dmr.results.csv.gz


title: TM22E-DMSO-PLX-A647


title: TM22E-DMSO-PLX-A546


title: PS24

description:
multiple.dmr.results.csv.gz
kidney.dmr.results.csv.gz
prostate.dmr.results.csv.gz
testis.dmr.results.csv.gz

value: no disease


title: TM22E-DMSO-CC-Neg-2


title: PS21


title: PS19

description: prostate.dmr.results.csv.gz


title: TCF1-CUT&RUN (exp2) resting Treg rep1

value: CD44-CD62L+ Foxp3+ CD4 T cells


title: PS17

description: prostate.dmr.results.csv.gz


title: RNA-seq activated Treg rep3

data_processing:
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align ChIP-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ChIP-seq duplicates: Picard v1.141
Call ChIP-seq peaks: MACS2 v2.1.1
Align CUT&RUN reads: STAR v2.5.0c [disable splicing alignment]
Remove CUT&RUN duplicates: Picard v1.141
Call CUT&RUN peaks: MACS2 v2.1.1
Genome_build: GRCm38 and CAST/EiJ
Supplementary_files_format_and_content: raw read count

extract_protocol:
Trizol extraction followed by SMART-Seq v4 Ultra Low Input RNA Kit
Kapa hyper prep kit


title: PS20

description: multiple.dmr.results.csv.gz


title: RNA-seq activated Treg rep2


title: TM22E-DMSO-CC-Neg-1


title: PS16

description: kidney.dmr.results.csv.gz


title: PS27

description: multiple.dmr.results.csv.gz


title: PS14

description: multiple.dmr.results.csv.gz


title: PS15


title: RNA-seq activated Treg rep1


title: PS30

description: multiple.dmr.results.csv.gz


title: TM22E-DMSO-CC-A647-2


title: TM22E-DMSO-CC-A647-1


title: RNA-seq resting Treg rep3


title: PS12


title: PS13


title: PS11


title: RNA-seq resting Treg rep2


title: TM22E-DMSO-CC-A546


title: smallRNAseq_K562_ZSWIM8_KO-10

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
The raw reads were trimmed using Cutadapt
Reads with base quality less than 30 at any position were dropped
The miRNA sequences were downloaded from miRBase v22
Each read was assigned to an miRNA according to the first 18nt.
TMM normalization and differential expression analysis is performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: a table of miRNA reads per million from edgeR analysis of these RNA-seq data

growth_protocol: K562 cells were grown in RPMI supplemented with 10% FBS and Antibiotic-Antimycotic solution, HEK293T and MEFs cells were grown in DMEM supplemented with 10% FBS and Antibiotic-Antimycotic solution

extract_protocol:
RNA was isolated using the miRNeasy Mini kit (Qiagen) for small RNA seq.
Total RNA was isolated from biological triplicates of each cell line using the miRNeasy Mini RNA isolation kit (Qiagen) including a DNase I digestion step to remove genomic DNA. Library preparation was performed following a previously published protocol (H. Kim et al., Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification. Nucleic Acids Res 47, 2630-2640 (2019)).

tag: sgrna received

value: no


title: PS9

description: testis.dmr.results.csv.gz

value: testis disease


title: RNA-seq resting Treg rep1


title: PS8

value: 1 year


title: PS18

value: Sperm


title: RNA-seq activated Tcon rep4

value: CD44+CD62L- Foxp3- CD4 T cells


title: PS7

value: MeDIP


title: Sample S1 technical replicate c

description: Saline rat 1 technical replicate c

value: Sprague-Dawley

value: Saline Rat

value: 15 physiological serum injections


title: smallRNAseq_K562_ZSWIM8_KO-8


title: PS10

value: pesticides


title: smallRNAseq_K562_ZSWIM8_KO-7


title: PS5


title: PS6


title: PS4

description: testis.dmr.results.csv.gz


title: RNA-seq activated Tcon rep3

value: B6/Cast F1


title: PS3

description: testis.dmr.results.csv.gz


title: smallRNAseq_K562_wild_type-3

value: wild type


title: RNA-seq activated Tcon rep1


title: PS2


title: smallRNAseq_K562_wild_type-2


title: PS1


title: RNA-seq resting Tcon rep3

value: CD44-CD62L+ Foxp3- CD4 T cells


title: smallRNAseq_K562_wild_type-1


title: RNA-seq resting Tcon rep2


title: RNA-seq resting Tcon rep1


title: 1105-19-sg9-HEK

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

data_processing:
Library strategy: DNA-seq
We directly analzed the fastq files using an online tool CRISPRESSO2.  We therefore do not have any additional processed data.

source_name: HEK cells

growth_protocol: DMEM grwoth medium supplemented with 10% FBS and 1% P/S

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation
targeted amplicon sequencing; two step PCR

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000

value: HEK

tag: treatment method

value: Lipofection

tag: treatment type


title: 1105-16-sg9-HEK


title: 1105-19-sg1-HEK


title: 1105-18-sg9-HEK


title: 1105-18-sg1-HEK


title: 1105-15-sg9-HEK_2


title: smallRNAseq_HEK293T_sgZSWIM8-2

value: CATCTCAAAATGGAAGACAT


title: ATAC-seq activated Treg rep4

extract_protocol:
Cell lysis, Nextera Tn5, Qiagen MinElute reaction cleanup
Nextera Tn5

value: CD44+CD62L- Foxp3+ CD4 T cells


title: 1105-16-sg1-HEK


title: smallRNAseq_HEK293T_sgZSWIM8-1


title: 1105-15-sg9-HEK_1


title: 1105-14-sg9-HEK


title: 1105-14-sg1-HEK


title: ATAC-seq activated Treg rep3


title: 1105-15-sg1-HEK


title: 1105-13-sg9-HEK


title: smallRNAseq_HEK293T_nontarget control-2

value: sgNT

value: ATCGTTTCCGCTTAACGGCG


title: smallRNAseq_HEK293T_nontarget control-3


title: ATAC-seq activated Treg rep2


title: ATAC-seq activated Treg rep1


title: 1105-11-sg9-HEK_2


title: 1105-11-sg9-HEK_1


title: 1105-13-sg1-HEK


title: smallRNAseq_HEK293T_nontarget control-1


title: smallRNAseq_HEK293T_sgZSWIM8-3


title: 1105-11-sg1-HEK_2


title: hyp.2G variant of p53 from subject c2, untreated, replicate 2

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: untreated LCL cell lines from subject c2 G334R variant G, replicate 2

data_processing:
RNA-Seq data was aligned using bowtie2 against hg19 version of genome and rsem (ver. 1.2.13) with Ensemble v84 transcriptome information used for gene count
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: MCF10A cell lines

extract_protocol:
Total RNA was extracted from MCF10A cells after 24 h of co-culture with MCF7 cell-derived sEV using Direct-zol RNA MiniPrep kit (Zymo Research). RNA quantity was determined using the Qubit 2.0 Fluorometer (ThermoFisher Scientific) and the quality was validated using the TapeStation RNA ScreenTape (Agilent).
One-hundred ng of total RNA was used to prepare a library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen)

tag: condition

value: hypoxia

tag: replcate


title: 1105-11-sg1-HEK_1


title: hyp.1G variant of p53 from subject c2, untreated, replicate 1

description: untreated LCL cell lines from subject c2 G334R variant G, replicate 1


title: 1105-10-sg1-HEK


title: ATAC-seq resting Treg rep2

value: CD44-CD62L+ Foxp3+ CD4 T cells


title: nor.2G variant of p53 from subject c1, untreated, replicate 2

description: untreated LCL cell lines from subject c1 G334R variant G, replicate 2

value: normoxia


title: 1105-10-sg9-HEK


title: 1105-09-sg1-HEK


title: ATAC-seq resting Treg rep1


title: 1105-09-sg9-HEK


title: 1105-07-sg9-HEK


title: 1105-06-sg9-HEK


title: 1105-06-sg1-HEK


title: ATAC-seq activated Tcon rep4

value: CD44+CD62L- Foxp3- CD4 T cells


title: nor.1G variant of p53 from subject c1, untreated, replicate 1

description: untreated LCL cell lines from subject c1 G334R variant G, replicate 1


title: 1105-05mut-sg1_1


title: ATAC-seq activated Tcon rep3


title: ATAC-seq activated Tcon rep2


title: ATAC-seq resting Treg rep4


title: 1105-07-sg1-HEK


title: 1105-05-sg9


title: Prog_treated_with_BAZ2B_Donor_A

city: Barcelona

first: Karthik

last: Arumugam

state: Barcelona

address: C/Dr.Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

data_processing:
After completion of the sequencing run, the fastq files were generated manually from the bcl files using a sample index sheet with the bcl2fastq software provided by Illumina. Data processing was done with a custom pipeline managed by Snakemake.
Reads where adapter-trimmed, filtered for low quality ones using fastp (https://doi.org/10.1093/bioinformatics/bty560) and aligned to GRCh38 using STAR ver. 2.5.2a in end-to-end mode and using --alignIntronMax 1 to prohibit splicing.
A number of mismatches up to 5% of the paired read length where allowed and only reads mapping uniquely and not onto chromosome M and blacklisted regions where retained for the following analyses.  PCR duplicates where removed using Picard Tools
Reads from pooled replicates of each sample where converted in BEDPE format and adjusted for Tn5 insertion. Peaks where called using MACS ver. 2.2.6  with “--nomodel”, “--call-summits”, “--nolambda”, “-f BEDPE” and “--keep-dup all” options
Genome_build: GRCh38
Supplementary_files_format_and_content: .narrowPeaks file

source_name: Umbilical cord blood

growth_protocol: Human CD34+ cells were sorted for Lineage-CD34+CD38+ progenitor cells. The cells were then cultured in serum-free enhanced media supplemented with two different formulations of recombinant human cytokines, (1) Stimulation media – contains SCF 300 ng/ml, FLT3 300 ng/ml, TPO 100 ng/ml, IL3 60 ng/ml (2) Maintenance media - SCF 100 ng/ml, FLT3 100 ng/ml, TPO 100 ng/ml, IL3 20 ng/ml, IL6 20 ng/ml. For experiments using the entire fraction of CD34+ cells, the cells were incubated in the stimulation media for 24 hours at 37 degrees C.

extract_protocol:
Samples were purified using a Zymo DNA clean and concentrator kit and eluted in 22 uL ultrapure water.
Appropriate sample indexing for 6-plex sequencing on an Illumina NextSeq were chosen for each library and the samples were amplified for 5 cycles to incorporate the sequencing adapters. A qPCR reaction was then performed to determine the optimal additional number of amplification cycles required for each sample to minimize PCR duplication, and each library was amplified for the appropriate number of additional cycles. No libraries exceeded a total of 11 PCR cycles.
After library amplification, the samples were again purified with the Zymo kit and eluted in 22 uL ultrapure water. Next, each library was run on a Novex-TBE 4-20% PAGE 10-well non-denaturing gel and subsequently stained with SYBR Gold. The gel was imaged and fragments within the range of 100-1000 bp were excised from the gel for each library. The libraries were recovered from the PAGE gel fragments using electroelution using D-tubes. The libraries were finally purified from the recovered TBE buffer using an Isopropanol/Acetate precipitation. Following the final purification of the libraries, quality control was done by perfoming a Bioanalyzer and KAPA qPCR library quantification assay. This allowed the determination of accurate library concentrations, after which the libraries were pooled, prepped for sequencing on an Illumina Nextseq 500/550 by standard methods using a 75 cycle High-output kit.

treatment_protocol: The cells were then infected for a first round with lentiviral vectors (Luciferase/BAZ2B) and incubated overnight in the stimulation media at 37 degrees C. The cells were then washed and resuspended in stimulation media. After approximately 4 hours the cells were re-infected for a second round with lentiviral vectors and continued incubation overnight at 37 degrees C. The cells were then washed and cultured in the maintenance media supplemented with 2 ug/ml of Doxycycline for the rest of the experiment. Every 2 days the cells were washed and re-plated in fresh media with doxycycline.

tag: individual

value: progenitors (Lin-CD34+CD38+)

tag: surface markers

value: Lineage-GFP+


title: 1105-05mut-sg1_2


title: Prog_treated_with_Luciferase_Donor_B

value: Luciferase


title: ATAC-seq activated Tcon rep1

tag: strain

tag: genotype


title: 1105-04-sg1

tag: cell line


title: 1105-04-sg9


title: Prog_treated_with_Luciferase_Donor_A

tag: cell type


title: ATAC-seq resting Treg rep3


title: Progenitors_day_0_Donor_B

tag: treatment

value: control


title: 1105-03-sg1


title: Prog_treated_with_BAZ2B_Donor_B


title: Progenitors_day_0_Donor_A


title: ATAC-seq resting Tcon rep2

value: B6/Cast F1


title: ATAC-seq resting Tcon rep3


title: 1105-02-sg9


title: 1105-02-sg1


title: 1105-01-sg1


title: 1105-01-sg9


title: ATAC-seq resting Tcon rep1


title: 1104-17-sg9


title: 1105-05-sg1


title: TDMD screen_Wild type-2_sorted_2nd run

description: sgRNA sequence amplified out of genomic DNA

data_processing:
Reads were mapped to Brunello library sgRNA reference files.
Reads from run1 and run2 were combined, and normalized read counts were calculated as described in Shalem et al., Science, 2014.
MAGeCK (Li et al., Genome Biology, 2014) was used to assign significance to each gene targeted by the sgRNAs in the Brunello library.
Genome_build: Brunello library sgRNA reference files obtained from Addgene
Supplementary_files_format_and_content: A table of normalized read counts for each sgRNA in each sample (run1 and run2 combined) is provided.

growth_protocol: K562 cells were grown in RPMI supplemented with 10% FBS and Antibiotic-Antimycotic solution

extract_protocol:
Genomic DNA was extracted from cell pellets using either a gDNA isolation method that has been previously described Golden et al., Nature, 2017 for the sorted cells or the MasterPureTM Complete DNA Purification Kit (Lucigen) for the unsorted cells.
PCR amplicon libraries were generated as described in the manuscript.
CRISPR/Cas9-mediated loss of function screening.

value: miR-7 reporter, wild type

value: brunello library


title: Foxp3 CUT&RUN bulk Treg rep3

value: Foxp3+ CD4 T cells


title: 1104-17-sg1

value: HEK

value: Lipofection


title: Foxp3 CUT&RUN bulk Treg rep2


title: TDMD screen_Wild type-2_unsorted_2nd run


title: TDMD screen_CYRANO KO-2_sorted_2nd run

value: miR-7 reporter, CYRANO-/-


title: TDMD screen_CYRANO KO-2_unsorted_2nd run


title: 1104-15-sg9


title: 1104-16-sg9


title: TDMD screen_Wild type-1_unsorted_2nd run


title: 1104-14-sg9


title: 1104-16-sg1


title: Foxp3 CUT&RUN bulk Treg rep1


title: 1105-03-sg9


title: 1104-14-sg1


title: ATAC-seq resting Tcon rep4

value: CD44-CD62L+ Foxp3- CD4 T cells


title: 1104-13-sg9


title: TDMD screen_Wild type-1_sorted_2nd run


title: 1104-13-sg1


title: Foxp3 ChIP-seq bulk Treg rep2

extract_protocol:
Covaris TruChIP Chromatin shearing kit
Kapa HTP


title: 1104-12-sg9


title: TDMD screen_CYRANO KO-1_unsorted_2nd run


title: 1104-11-sg9


title: 1104-12-sg1


title: 1104-11-sg1


title: Foxp3 ChIP-seq bulk Treg rep1


title: RNA-seq CD73- Thymic Foxp3-GFPKO rep3

extract_protocol:
Trizol extraction followed by SMART-Seq v4 Ultra Low Input RNA Kit
KAPA Hyper Prep Kit

value: CD73- Foxp3-GFPKO+ CD4SP Thymocytes


title: TDMD screen_CYRANO KO-1_sorted_2nd run


title: TDMD screen_Wild type-2_unsorted


title: 1104-15-sg1


title: RNA-seq CD73- Thymic Foxp3-GFPKO rep2


title: RNA-seq CD73- Thymic Foxp3-GFPKO rep1


title: TDMD screen_Wild type-2_sorted


title: 1104-04-sg9


title: TDMD screen_CYRANO KO-2_unsorted


title: 1104-05-sg1


title: 1104-03-sg9


title: 1104-04-sg1


title: RNA-seq CD73- Thymic Treg rep3

value: CD73- Foxp3+ CD4SP Thymocytes


title: TDMD screen_CYRANO KO-2_sorted


title: RNA-seq CD73- Thymic Treg rep2


title: Foxp3 ChIP-seq bulk Treg rep3


title: 1104-03-sg1


title: 1104-02-sg9


title: TDMD screen_Wild type-1_unsorted


title: 1104-02-sg1


title: RNA-seq CD73- Thymic Treg rep1


title: 1104-07-sg1


title: RNA-seq activated Foxp3-GFPKO rep3

value: CD44+CD62L- Foxp3-GFPKO+ CD4 T cells


title: 1104-01-sg1


title: HEK-FANCA-HNHx-ABE8e-001

value: FANCA


title: TDMD screen_CYRANO KO-1_unsorted


title: HEK-FANCA-HNHx-ABE8e-002


title: 1104-07-sg9


title: TDMD screen_CYRANO KO-1_sorted


title: RNA-seq activated Foxp3-GFPKO rep2


title: 1104-05-sg9


title: HEK-FANCA-ABE710-NGG-003


title: smallRNAseq_ZSWIM8 KO-3

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
The fastq files are checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Fastq files are mapped to hg19 reference genome (from igenomes) using STAR
Read counts are then generated using featureCounts
TMM normalization and differential expression analysis is performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: a table of edgeR analysis of these RNA-seq data

extract_protocol:
RNA was isolated using the miRNeasy Mini kit (Qiagen) for small RNA seq.
Small RNA seq library preparation and next generation sequencing were performed by DNA Link using NEB Next Small RNA Library Prep for Illumina (New England BioLabs)

value: no


title: RNA-seq activated Treg GFP-DTR/WT rep2

value: CD44+CD62L- Foxp3+ CD4 T cells


title: HEK-FANCA-ABE710-NGG-001


title: smallRNAseq_ZSWIM8 KO-1


title: HEK-FANCA-ABE8e-RY1-003


title: TDMD screen_Wild type-1_sorted


title: RNA-seq activated Treg GFP-DTR/WT rep3


title: 1104-01-sg9


title: smallRNAseq_ZSWIM8 KO-2


title: RNA-seq activated Treg GFP-DTR/WT rep1


title: HEK-FANCA-ABE8e-RY1-002


title: HEK-FANCA-ABE8e-RY1-001


title: smallRNAseq_WT-2

value: wild type


title: HEK-FANCA-ABE8e-NGG-002


title: RNA-seq resting Foxp3-GFPKO rep3

value: CD44-CD62L+ Foxp3-GFPKO+ CD4 T cells


title: HEK-FANCA-ABE710-NGG-002


title: HEK-FANCA-ABE8e-NGG-001


title: RNA-seq resting Foxp3-GFPKO rep2


title: HEK-HNHx-ABE8e-18-002


title: HEK-FANCA-ABE8e-RY2-003


title: HEK-FANCA-ABE8e-RY2-002


title: smallRNAseq_sgCYRANO-3

value: sgCYRANO

value: CATCTCAAAATGGAAGACAT


title: RNA-seq activated Foxp3-GFPKO rep1

value: B6/Cast F1


title: HEK-HNHx-ABE8e-18-001


title: HEK-FANCA-ABE8e-RY2-001


title: smallRNAseq_WT-1


title: HEK-HNHx-710-18-003


title: HEK-HNHx-710-18-002


title: smallRNAseq_sgCYRANO-2


title: HEK-HNHx-710-18-001


title: HEK-FANCA-ABE8e-NGG-003


title: RNA-seq resting Treg GFP-DTR/WT rep3

value: CD44-CD62L+ Foxp3+ CD4 T cells


title: smallRNAseq_WT-3


title: RNA-seq resting Treg GFP-DTR/WT  rep2


title: smallRNAseq_sgCYRANO-1


title: HEK-Abemx710-18-002


title: RNA-seq resting Treg GFP-DTR/WT  rep1


title: HEK-Abemx710-18-001


title: smallRNAseq_sgNT-3

value: sgNT

value: ATCGTTTCCGCTTAACGGCG


title: RNA-seq resting Foxp3-GFPKO rep1


title: smallRNAseq_sgNT-2


title: HEK-Abe8e-18-003

value: HEK

value: Lipofection


title: HEK-Abe8e-18-001


title: ATAC-seq activated Foxp3-GFPKO rep2


title: ATAC-seq activated Foxp3-GFPKO rep3


title: HEK-Abe8e-18-002


title: smallRNAseq_sgNT-1


title: HEK-K11-HNHx-710-001


title: HEK-K11-HNHx-710-003


title: ATAC-seq activated Treg GFP-DTR/WT rep3


title: HEK-HNHx-ABE8e-11-ABE8e-003


title: HEK-HNHx-ABE8e-11-ABE8e-002


title: ATAC-seq activated Foxp3-GFPKO rep1


title: ST1387_UT_Pol2

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

description:
Chromatin IP and Sequencing of FLS cells treated with DMSO.
RA FLS Cells

data_processing:
Mapping of 75bp sequencing reads with BWA using default settings.
Reads that had greater than 2 mismatches and multimapping reads were removed followed by removal of PCR duplicates through deduplication with samtools.
Peak calling was performed with MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: bigWig fold enrichment over input files.

source_name: Fibroblast like Synoviocytes

growth_protocol: RA-FLS (n=2 donors) were seeded at 6x10e6/T225 flasks and treated with JQ1+ (1 µM) or DMSO and stimulated with IL-1β at 1 ng/ml.

extract_protocol:
Cell pellets were resuspended in ice cold wash buffer PBS-Igepal and centrifuged again to pellet cells. Repeat the wash step one more time with 1 mM PMSF in the wash buffer. Cells were centrifuged and pellets snap frozen in dry ice and stored at -80oC. Cell pellets were sent to Active Motif (CA, USA) for ChIPseq analysis.
Illumina Library Preparation.

treatment_protocol: After 24 hr incubation, cells were fixed with paraformaldehyde for 15 min with agitation at room temperature and the cross-linking reaction was terminated by incubation of cells with glycine for 5 min. Cells were rinsed twice with ice cold PBS, scraped from flasks with a cell scraper and centrifuged for 5 min, 4oC, 1000xg.

tag: diagnosis

value: Rheumatoid arthritis

value: Fibroblast like Synoviocytes

value: DMSO

tag: chip antibody

tag: donor


title: ST1387_Input

description:
Input Control.
RA FLS Cells


title: HEK-Abemx710-18-003


title: HEK-HNHx-ABE8e-11-ABE8e-001


title: HEK-Abe8e-11-003


title: HEK-Abemx710-11-002


title: ST1387_UT_BRD4


title: ATAC-seq activated Treg GFP-DTR/WT rep1


title: ATAC-seq activated Treg GFP-DTR/WT rep2


title: HEK-Abe8e-11-002


title: ATAC-seq resting Foxp3-GFPKO rep2


title: HEK-Abe8e-11-001


title: ST1387_JQ_Pol2

description:
Chromatin IP and Sequencing of FLS cells treated with JQ1.
RA FLS Cells


title: HEK-HNHx-ABE8e-10-003


title: HEK-HNHx-ABE8e-10-002


title: ATAC-seq resting Foxp3-GFPKO rep1


title: HEK-HNHx-ABE8e-10-001


title: ATAC-seq resting Treg GFP-DTR/WT rep3


title: ST1387_JQ_BRD4


title: HEK-HNHx-710-10-003


title: ST1387_JQ_BRD2


title: HEK-HNHx-710-10-002


title: ATAC-seq resting Treg GFP-DTR/WT rep2


title: HEK-HNHx-710-10-001


title: HEK-Abemx710-11-003


title: ATAC-seq resting Treg GFP-DTR/WT rep1


title: HEK-K11-HNHx-710-002


title: HEK-Abemx710-10-002


title: ST1412_UT_Pol2


title: HEK-Abemx710-10-001


title: HEK-Abe8e-10-003


title: TCF1-CUT&RUN activated Foxp3-GFPKO rep3

value: CD44+CD62L- Foxp3-GFPKO+ CD4 T cells


title: ST1412_UT_BRD4


title: TCF1-CUT&RUN activated Foxp3-GFPKO rep2


title: HEK-Abe8e-10-002


title: ST1412_UT_BRD2


title: HEK-HNHx-ABE8e-8-003


title: TCF1-CUT&RUN activated Foxp3-GFPKO rep1


title: HEK-HNHx-ABE8e-8-002


title: ST1412_JQ_Pol2


title: HEK-HNHx-ABE8e-8-001


title: HEK-HNHx-710-8-001


title: HEK-HNHx-710-8-002


title: TCF1-CUT&RUN activated Treg rep3


title: HEK-Abemx710-10-003


title: TCF1-CUT&RUN activated Treg rep2


title: ST1412_JQ_BRD2


title: TCF1-CUT&RUN resting Foxp3-GFPKO rep3


title: HEK-Abemx710-8-001


title: TCF1-CUT&RUN activated Treg rep1


title: ST1399_JQ1

description:
Transcriptomics of FLS cells treated with JQ1.
RA FLS cells.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

data_processing:
QC with Fastqc.
Alignment: Omicsoft aligner B37.3 Human Genome Model.
Quantification with omicsoft gene model using an EM algorithm.
Genome_build: B37.3
Supplementary_files_format_and_content: final_FLS_JQ1_genecounts.txt: Tab-delimited text file includes gene counts.
Supplementary_files_format_and_content: final_FLS_JQ1_transcriptcounts.txt: Tab-delimited text file includes transcript counts.

growth_protocol: RA-FLSs were seeded at 8000 cells/well in a 96-well plate. After 24 hr JQ1+ or control JQ1- were added at concentrations ranging from 0.01 µM to 10 µM generated with 3-fold dilution of the compounds. At the same time cells were also stimulated with 1ng/ml IL-1β (R&D Systems, MN, USA). After overnight incubation, BrdU was added for a few hours and proliferation was quantitated by BrdU ELISA as per manufacturer's protocol (Roche Diagnostics, Basel, Switzerland).

extract_protocol:
RA-FLS (3 RA and 3 healthy donors) were seeded at 3x10e5/well in a 6-well plate with 2 ml media and incubated overnight for cells to attach. Cells were treated with JQ1+ (1 µM) or DMSO and stimulated with 1 ng/ml IL-1β. After 24 hour incubation, cell media were removed and 600 µl RLT lysis buffer containing β-mercaptoethanol (1%) was added to wells for RNA extraction using RNeasy plus mini kit (Qiagen, Hilden, Germany). RNA was extracted from cell cultures with the Qiagen RNeasy Kit (Qiagen, Hilden, Germany).
RNA samples (40 ng) were reverse transcribed and sequencing libraries constructed using NuGen Ovation Universal RNA-Seq System (CAT# 0402-A01) according to the manufacturer’s protocol. The resulting sequencing libraries were analyzed using the Caliper LabChip GX and quantified using KAPA qPCR. Libraries were then normalized and pooled in batches of 8. Each pool of 8 samples was clustered and sequenced on an Illumina NextSeq500 instrument using 2x100 bp paired end reads, following the manufacturer’s protocols. Each library was loaded to obtain ~80 million reads.


title: ST1412_Input

description:
Input Control.
RA FLS Cells


title: HEK-Abe8e-10-001


title: HEK-Abe8e-8-003


title: ST1399_JQ1_IL1b

description:
Transcriptomics of FLS cells treated with JQ1 and IL1b.
RA FLS cells.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

value: JQ1 and IL1b


title: HEK-Abe8e-8-002


title: TCF1-CUT&RUN resting Foxp3-GFPKO rep2


title: HEK-Abe8e-8-001


title: ST1399_DMSO

description:
Transcriptomics of FLS cells treated with DMSO.
RA FLS cells.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt


title: HEK-HNHx-710-8-003


title: HEK-HNHx-ABE8e-7-003


title: HEK-Abemx710-8-003


title: TCF1-CUT&RUN resting Foxp3-GFPKO rep1


title: ST1399_DMSO_IL1b

description:
Transcriptomics of FLS cells treated with DMSO and IL1b.
RA FLS cells.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

value: DMSO and IL1b


title: ST1412_JQ_BRD4


title: HEK-HNHx-ABE8e-7-001


title: TCF1-CUT&RUN resting Treg rep2


title: ST1387_JQ1


title: HEK-Abemx710-8-002


title: HEK-HNHx-710-7-002


title: ST1387_JQ1_IL1b


title: HEK-HNHx-710-7-001


title: HEK-ABE8e-7-003


title: ST1387_DMSO


title: HEK-HNHx-ABE8e-7-002


title: TCF1-CUT&RUN resting Treg rep1


title: HEK-ABE8e-7-002


title: ATAC-seq Tcf7 heterozygous resting Foxp3-GFP-Cre-KO rep3

source_name: Foxp3ΔEGFPiCre/WT Tcf7fl/WT

value: Foxp3 delta_EGFPiCre/WT Tcf7fl/WT

value: Foxp3 reporter-null+ CD4 T cells


title: HEK-ABE8e-7-001


title: HEK-HNHx-ABE8e-1-002


title: HEK-HNHx-ABE8e-1-001


title: ATAC-seq Tcf7 heterozygous resting Foxp3-GFP-Cre-KO rep2


title: ST1387_DMSO_IL1b


title: ST1385_JQ1

description:
Transcriptomics of FLS cells treated with JQ1.
FLS cells from healthy donors.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

value: Healthy


title: HEK-HNHx-ABE8e-1-003


title: ST1387_UT_BRD2


title: HEK-HNHx-710-1-003


title: ST1385_JQ1_IL1b

description:
Transcriptomics of FLS cells treated with JQ1 and IL1b.
FLS cells from healthy donors.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt


title: HEK-HNHx-710-1-001


title: HEK-HNHx-710-1-002


title: TCF1-CUT&RUN resting Treg rep3


title: ATAC-seq Wild-type resting Foxp3-GFP-Cre-KO rep3

source_name: Foxp3ΔEGFPiCre/WT Tcf7WT/WT

value: Foxp3 delta_EGFPiCre/WT Tcf7WT/WT


title: ATAC-seq Tcf7 heterozygous resting Foxp3-GFP-Cre-KO rep1


title: ST1385_DMSO

description:
Transcriptomics of FLS cells treated with DMSO.
FLS cells from healthy donors.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt


title: HEK-HNHx-ABE8e-18-003


title: HEK-Abe8e-1-002


title: ATAC-seq Wild-type resting Foxp3-GFP-Cre-KO rep2


title: HEK-HNHx-710-7-003


title: HEK-Abe8e-1-003


title: 1102-20sg7HEK-2


title: ST1385_DMSO_IL1b

description:
Transcriptomics of FLS cells treated with DMSO and IL1b.
FLS cells from healthy donors.
mRNA
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt


title: ATAC-seq Wild-type resting Foxp3-GFP-Cre-KO rep1


title: 1102-19sg7HEK-1


title: ST1359_JQ1


title: 1102-17sg7HEK-2


title: 1102-18sg7HEK-2


title: RNA-seq Tcf7 heterozygous resting Foxp3-GFP-Cre-KO rep3


title: ST1359_JQ1_IL1b


title: RNA-seq Tcf7 heterozygous resting Foxp3-GFP-Cre-KO rep2


title: 1102-16sg7HEK-2


title: ST1359_DMSO


title: 1102-14sg7HEK-2


title: RNA-seq Tcf7 heterozygous resting Foxp3-GFP-Cre-KO rep1


title: 1102-15sg7HEK-2


title: RNA-seq Wild-type resting Foxp3-GFP-Cre-KO rep3


title: ST1359_DMSO_IL1b


title: Flayed2 5mm flower bud b

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

description: Small RNAs

data_processing: Small RNA reads were quality-controled, adaptor-trimmed and collapsed into tag-count format

organism: Erythranthe lewisii

source_name: Flayed2 5mm flower bud b

growth_protocol: Plants were grown in the University of Connecticut research greenhouses under natural light supplemented with sodium vapor lamps, ensuring a 16-hr day length.

extract_protocol:
Total RNA was extracted using Trizol (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EMS mutagenesis was performed using the Mimulus lewisii Pursh inbred line LF10 as described (Owen and Bradshaw, 2011). Another inbred line SL9 was used to generate the “flayed x SL9” F2 populations.

tag: tissue

value: 5mm Flower bud

tag: genotype/variation

value: flayed2 mutant


title: ST1305_JQ1


title: 1102-12sg7HEK-2


title: HEK-Abe8e-1-001


title: RNA-seq Wild-type resting Foxp3-GFP-Cre-KO rep2


title: Flayed1 5mm flower bud b

description: Small RNAs

source_name: Flayed1 5mm flower bud b

value: flayed1 mutant


title: Flayed2 5mm flower bud

description: Small RNAs

source_name: Flayed2 5mm flower bud


title: ST1305_JQ1_IL1b


title: Melanocyte_NI_Rep3

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

description:
Biological replicate #3 (cells from 4 males pooled)
Melanocyte3

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm10) using STAR (version 2.5.2a).
Expression values of each gene were quantified as transcript per million (TPM), as well as by raw counts, using Salmon (version 0.8.2) and Tximport (version 1.8.0).
Genome_build: mm10 (UCSC release)
Supplementary_files_format_and_content: tab-delineated text files contain raw counts for all samples

source_name: Mouse back skin

extract_protocol:
FACS purified cells were sorted into TRI Reagent LS in 2ml collection tubes. Total RNA was purified using the Direct-zol RNA MicroPrep kit from Zymo research.
RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit. Libraries were sequenced on an Illumina HiSeq 4000 instrument.

tag: cell stage

value: Melanocytes

tag: Sex

value: Male

tag: age

tag: hair cycle stage

value: Full anagen

value: Dct-EGFP+ Lef1-RFP+ (CD1/C57Bl6J mix)

tag: sorting strategy

value: Dct-eGFP+, Lef1-RFP+, c-Kit+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca-1-, and CD34-


title: ST1305_DMSO

value: Fibroblast like Synoviocytes


title: 1102-10sg7HEK-2

value: HEK

tag: treatment method

value: Lipofection

tag: treatment type


title: Flayed1 5mm flower bud

description: Small RNAs

source_name: Flayed1 5mm flower bud


title: RNA-seq Wild-type resting Foxp3-GFP-Cre-KO rep1

tag: strain


title: LF10 5mm flower bud b

description: Small RNAs

source_name: LF10 5mm flower bud b

value: wild type (LF10 inbred line)


title: 1102-11sg7HEK-2


title: ST1305_DMSO_IL1b

value: DMSO and IL1b


title: 1102-08sg7HEK-1


title: LF10 5mm flower bud

description: Small RNAs

source_name: LF10 5mm flower bud


title: ST1303_JQ1

description:
Transcriptomics of FLS cells treated with JQ1.
FLS cells from healthy donors.
mRNA
ST1303_JQ_S8_001
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt


title: 1102-09sg7HEK-2


title: Melanocyte_NI_Rep2

description:
Biological replicate #2 (cells from 2 males pooled)
Melanocyte2


title: Melanocyte_NI_Rep1

description:
Biological replicate #1 (cells from 3 males pooled)
Melanocyte1


title: ST1303_JQ1_IL1b

description:
Transcriptomics of FLS cells treated with JQ1 and IL1b.
FLS cells from healthy donors.
mRNA
ST1303_JQ_IL_1b_S8_001
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

value: JQ1 and IL1b


title: 1102-07sg7HEK-1


title: ST1303_DMSO

description:
Transcriptomics of FLS cells treated with DMSO.
FLS cells from healthy donors.
mRNA
ST1303_DMSO_S7_001
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

value: DMSO


title: 1102-05sg7HEK-2


title: ST1303_DMSO_IL1b

description:
Transcriptomics of FLS cells treated with DMSO and IL1b.
FLS cells from healthy donors.
mRNA
ST1303_DMSO_IL_1b_S7_001
processed data file: final_FLS_JQ1_genecounts.txt
processed data file: final_FLS_JQ1_transcriptcounts.txt

value: Healthy


title: qMcSC_NI_Rep1

description:
Biological replicate #1 (cells from 4 males pooled)
MelanocyteSC1

value: Quiescent melanocyte stem cells

value: 2nd telogen

value: Dct-eGFP+ (CD1/C57Bl6J mix)

value: Dct-eGFP+, integrin α6medium-low, dump (CD31, CD45, CD140a)-, Sca1-, and CD34-


title: qMcSC_NI_Rep2

description:
Biological replicate #2 (cells from 4 males pooled)
MelanocyteSC2


title: Mt08 Avi+Lipos

city: Badalona

first: Lauro

last: Sumoy

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

department: High Content Genomics and Bioinformatics

institute: IGTP

data_processing:
Demultiplexed fastq raw sequencing data files were the default output of a NextSeq 500 genetic analyzer (SBS-based sequencing technology, Illumina, San Diego, CA, USA)s
Per sample read quality was assessed using the fastx_quality stats software (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Trimming of Illumina reads was performed using the tool Trimmomatic V0.30 (http://www.usadellab.org/cms/?page=trimmomatic)
We used Tophat v2.1.0 (http://ccb.jhu.edu/software/tophat/index.shtml) [3], which uses Bowtie v2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), to map RNA-seq reads to the reference genome.
Using BAM files obtained from mapping all reads per sample and the GTF file with the annotation of exons, we applied featureCounts (http://bioinf.wehi.edu.au/featureCounts/) [4] to count how many reads map to each feature.
Statistically significant differences in miRNA expression were determined both by DESeq2 (Love, 2014) with multiple testing adjustment.
Genome_build: Ensembl release 78 (Homo_sapiens.GRCh38.dna.primary_assembly) human reference genome
Supplementary_files_format_and_content: Processed RNA expression profiling (human gene symbol HGNC_Id from ENSEMBL) data table provided as a supplementary file in excel workbook (.xlsx) format. Header details: (1) Index, unique numerical identifier; (2) Gene, ENSEMBL ID at gene level; (3) hgnc_symbol_ID, Human Gene Nomenclature Comiitte gene symbol; (4) description, gene description;(5) gene_biotype, RNA classification by byotype; (6) uniprot_IDs, Uniprot associated protein identifier; (7) uniprotswissprot_IDs, Swissprot collection protein identifier in Uniprot; (8) baseMean, average abundance measure DESeq2 derived average of normalized read counts for all samples. Following (9-24)are normalized count values for all 20 samples (4 conditions, 4 samples per condition): (9) Mt01.Ctrl; (10) Mt03.Ctrl; (11) Mt05.Ctrl; (12) Mt08.Ctrl; (13) Mt01.LIPOS; (14) Mt03.LIPOS; (15) Mt05.LIPOS; (16) Mt08.LIPOS; (17) Mt01.AVI; (18) Mt03.AVI; (19) Mt05.AVI; (20) Mt08.AVI; (21) Mt01.A.L; (22) Mt03.A.L;(23) Mt05.A.L; (24) Mt08.A.L. Individuals: Mt01, Mt03, Mt05, and Mt08. Conditions: Ctrl, control; LIPOS, liposome only; AVI, Liraglutide only; A.L., Liraglutide plus liposome. Finally there are 15 columns with summary statistics for each comparison (5 comparisons, 3 measures per comparison): (25) log2FoldChange_LIPOSvsC; (26) pvalue_LIPOSvsC; (27) padj_LIPOSvsC; (28) log2FoldChange_AVIvsC; (29) pvalue_AVIvsC; (30) padj_AVIvsC; (31) log2FoldChange_ALvsC; (32) pvalue_ALvsC; (33) padj_ALvsC; (34) log2FoldChange_ALvsLIPOS; (35) pvalue_ALvsLIPOS; (36) padj_ALvsLIPOS; (37) log2FoldChange_AVIvsAL; (38) pvalue_AVIvsAL; (39) padj_AVIvsAL Comparions include: LIPOSvsC, liposomes alone versus control; AVIvsC, Liraglutide alone versus control; ALvsC, Liraglutide plus liposomes versus control; ALvsLIPOS, Liraglutide plus liposomes versus liposomes alone; and  AVIvsAL, Liraglutide alone versus Liraglutide plus liposomes alone. Measures include default output from DESeq2: log2FoldChange, logarithm in base 2 of count ratios; pvalue, nominal p value; padj, adjusted p value (by default Benjamini and Hochberg method).

source_name: peripheral blood

growth_protocol: Human monocytes (CD14+) were isolated from human PBCMs of subjects with type 1 diabetes, then they were cultured during 4h with the below referred treatments.

extract_protocol:
RNEasy MicroKit (Qiagen, Germany)
NebNext, Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA)

treatment_protocol: huDCs were cultured during 4h with either PBS, Liraglutide 1000nM, PSAB-liposomes or PSAB-liposomes+Liraglutide.

tag: individual id

value: Subject 08

tag: disease state

value: Type 1 Diabetes

value: monocyte-derived dendritic cells

tag: treatment (cultured with)

value: PSAB-liposomes + Liraglutide


title: 1102-03sg7HEK-2

tag: cell line


title: p7 KO replicate 2

city: Illkirch

middle: D

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
reads were mapped to the mm10 Esembl96 version using STAR 2.7.0f (--outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 10)
reads were counted using htseq/0.9.1 (--mode=intersection-nonempty --stranded=no --minaqual=10 --type=exon --idattr=gene_id --nonunique=none)
differential expression analysis was performed using DESeq2 1.22.2 using Rstudio 1.1.456 and R 3.5.3
Genome_build: mm10, Ensembl v96
Supplementary_files_format_and_content: differential expression data

source_name: total RNA from hand-picked primary follicles oocytes from p7 Tbp2 mutant ovaries (340 oocytes ~5.8 ng RNA)

extract_protocol: RNA was extracted using NucleoSpin RNAXS kit (Macherey Nagel) according to the manufacturer's instructions

value: oocytes

tag: follicle stage

value: primary

tag: mouse age

tag: genotype

value: Tbp2 null


title: p7 KO replicate 1

source_name: total RNA from hand-picked primary follicles oocytes from p7 Tbp2 mutant ovaries (280 oocytes ~3.6 ng RNA)

tag: tissue


title: p7 KO replicate 3

source_name: total RNA from hand-picked primary follicles oocytes from p7 Tbp2 mutant ovaries (251 oocytes ~5.8 ng RNA)


title: 1102-06sg7HEK-2

source_name: HEK cells

value: HEK

value: Lipofection


title: Mt08 AVI

tag: cell type

value: Liraglutide


title: p7 WT replicate 3

source_name: total RNA from hand-picked primary follicles oocytes from p7 wild-type ovaries (400 oocytes ~5.9 ng RNA)

value: WT


title: 12d-TNFa+withdraw-10d+TNFa-9h Tet-TKO RNA-seq, rep1

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

description:
embryonic kidney cells
somatic cell
MGISEQ-2000
mRNA

data_processing:
RNA-seq basecalls performed by BGI, Shenzhen.
RNA-Seq data were mapped to Human Gencode release 24 by STAR aligner and quantified by Cuffdiff.
ChIP-seq basecalls performed by Berry Genomics, Co. Ltd. Beijing.
ChIP reads were mapped to UCSC hg38 genome by Bowtie2 (2.3.4.2).
ChIP data were filtered using samtools rmdup to remove potential PCR duplicates.
Enzymatic Methyl-seq reads in PE150 were firstly assessed by FASTQC software and then trimmed by trim_galore to remove adapters and low-quality bases. The filtered reads were then mapped to human genome (hg38) using the Bismark software (v0.22.3). Duplicate reads were discarded, and methylation information were called by Bismark.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM values were calculated by Cuffdiff and stored as tab-separated texts.
Supplementary_files_format_and_content: bigWig files were generated using IGV tools with fragment extension of average fragments size.

extract_protocol:
Total RNA of cells was isolated using RNeasy Mini Kit (Qiagen), and cDNA were synthesized using PrimeScript first strand cDNA synthesis kit (Takara) with oligo-dT.
The RNA-seq libraries were constructed by BGI, Shenzhen, as the platform BGISEQ-500 instruction described.
ChIP-seq were performed as previously described (Xiong et al., Molecular Cell 64, 913-925).
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB). DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).
The NEBNext Enzymatic Methyl-seq Conversion Module (NEB E7125L) was used for measuring genome-wide DNA methylation level. Purified genomic DNA containing 0.05% CpG methylated pUC19 control DNA and 1% unmethylated lambda DNA was sheared to a mean length of 450 bp with Covaris M220 Focused-ultrasonicator. End repair, A-tailing, methylated adaptor ligation and size selection were performed on 125 ng fragmented genomic DNA with Kapa hyper prep kit (Kapa Biosystems KK8504) according to the manufacturer’s instructions. The methylated adaptor ligated DNA fragments were then treated with oxidation of 5mC and 5hmC, clean-up of TET2 converted DNA, denaturation of DNA, deamination of cytosines and clean-up of deaminated DNA using the NEBNext Enzymatic Methyl-seq Conversion Module (NEB E7125L). The deaminated DNA was amplified with KAPA HiFi Hotstart Uracil+ ReadyMix PCR kit using primers from NEBNext multiplex oligos for Illumina (index primers set 1) (NEB E7335) (Kapa Biosystems KK2801) according to the manufacturer’s protocol. PCR cycling condition was as follows: 98℃ for 45 s, followed by 7 cycles of 98℃ for 15 s, 60℃ for 30 s, 72℃ for 30 s, and final extension 72℃ for 1 min, then hold at 4℃. Libraries were sequenced on an Illumina NovaSeq 6000 using 150-bp paired-end mode.

treatment_protocol:
The final concentration of TNF (high, default) is 50 ng/mL.
The final concentration of TNF (low, specified) is 0.4 ng/mL.

value: TET1/2/3-TKO of HEK 293 transfected with reporter construct

tag: treatment

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days, and add TNF-alpha 9 hours


title: 1102-02sg7HEK-2


title: 12d-TNFa+withdraw-10d Tet-TKO RNA-seq, rep1

source_name: 12d-TNFa+withdraw-10d Tet-TKO cells

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days


title: Mt08 Control

value: PBS


title: 1102-04sg7HEK-2


title: 1102-13sg7HEK-2


title: p7 WT replicate 2

source_name: total RNA from hand-picked primary follicles oocytes from p7 wild-type ovaries (350 oocytes ~8.2 ng RNA)


title: 9h-TNFa treated Tet-TKO RNA-seq, rep2

source_name: 9h-TNFa treated Tet-TKO cells

value: TNF-alpha treatment 9 hours


title: Mt05 Avi+Lipos

value: Subject 05


title: p7 WT replicate 1

source_name: total RNA from hand-picked primary follicles oocytes from p7 wild-type ovaries (400 oocytes ~5 ng RNA)


title: 9h-TNFa treated Tet-TKO RNA-seq, rep1


title: Mt05 AVI


title: non-treated Tet-TKO RNA-seq, rep2

source_name: non-treated Tet-TKO cells

value: no treatment


title: dABEmx7-10-sg4-Rep1


title: dABEmx7-10-sg4-Rep3


title: p14 KO replicate 1

source_name: total RNA from hand-picked secondary follicles oocytes from p14 Tbp2 mutant ovaries  (136 oocytes  ~2.8 ng RNA)

value: secondary


title: Mt03 Avi+Lipos

value: Subject 03

value: Type 1 Diabetes

value: monocyte-derived dendritic cells


title: 12d-TNFa+withdraw-10d+TNFa-9h WT RNA-seq, rep2

source_name: 12d-TNFa+withdraw-10d+TNFa-9h WT cells

value: HEK 293 transfected with reporter construct


title: p14 KO replicate 2

source_name: total RNA from hand-picked secondary follicles oocytes from p14 Tbp2 mutant ovaries  (130 oocytes  ~6.2 ng RNA)

value: oocytes

value: Tbp2 null


title: Mt05 Control


title: Mt03 Lipos

value: PSAB-liposomes


title: ABEdHNH7-10-sg4-Rep2

value: HEK

value: Lipofection


title: 12d-TNFa+withdraw-10d WT RNA-seq, rep2

source_name: 12d-TNFa+withdraw-10d WT cells


title: 12d-TNFa+withdraw-10d+TNFa-9h Tet-TKO RNA-seq, rep2

value: TET1/2/3-TKO of HEK 293 transfected with reporter construct


title: 12d-TNFa+withdraw-10d+TNFa-9h WT RNA-seq, rep1

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days, and add TNF-alpha 9 hours


title: 1102-01sg7HEK-1


title: Mt03 AVI

value: Liraglutide


title: p14 WT replicate 1

source_name: total RNA from hand-picked secondary follicles oocytes from p14 WT ovaries (200 oocytes ~5.1 ng RNA)

value: WT


title: dABEmx7-10-sg4-Rep2


title: Mt03 Control

value: PBS


title: non-treated Tet-TKO RNA-seq, rep1


title: 12d-TNFa+withdraw-10d Tet-TKO RNA-seq, rep2

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days


title: Mt05 Lipos

value: Subject 05


title: p14 KO replicate 3

source_name: total RNA from hand-picked secondary follicles oocytes from p14 Tbp2 mutant ovaries  (214 oocytes  ~11.3 ng RNA)

value: secondary


title: ABEdHNH7-10-sg4-Rep3


title: dABEmax7-10-sg1-Rep2


title: Mt01 Avi+Lipos

source_name: peripheral blood

value: Subject 01

value: PSAB-liposomes + Liraglutide


title: dABEmax7-10-sg1-Rep1


title: p14 WT replicate 2

source_name: total RNA from hand-picked secondary follicles oocytes from p14 WT ovaries (144 oocytes  ~2.6 ng RNA)


title: MUT2

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Genome_build: mm10
Supplementary_files_format_and_content: txt files of normalized gene counts for each sample

source_name: Colon

extract_protocol:
tumor-filled colon were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 18 weeks


title: MUT1


title: ABEdHNH7-10-sg1-Rep3


title: non-treated WT RNA-seq, rep2

source_name: non-treated WT cells

value: HEK 293 transfected with reporter construct

value: no treatment


title: ABEdHNH7-10-sg1-Rep2

source_name: HEK cells


title: p14 WT replicate 3

source_name: total RNA from hand-picked secondary follicles oocytes from p14 WT ovaries (260 oocytes ~7.3 ng RNA)

value: oocytes


title: 12d-TNFa+withdraw-10d WT RNA-seq, rep1


title: WT3

value: wild type


title: ABEdHNH7-10-sg1-Rep1

value: HEK


title: WT2


title: dABEmax7-10-sg1-Rep3

value: Lipofection


title: 12h-high-TNFa treatment on pretreatment, RNAseq, rep2

source_name: 12h-high-TNFa treatment on pretreated cells

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days, and add 50 ng/mL TNF-alpha 12 hours


title: PI3-sg7-Rep3


title: WT1


title: PI3-sg7-Rep2


title: 9h-TNFa treated WT RNA-seq, rep1

source_name: 9h-TNFa treated WT cells

value: TNF-alpha treatment 9 hours


title: PARP3KO_ASTRO_3

first: Françoise

last: DANTZER

address: 300 boulevard S. Brant

institute: CNRS

description: processed data file: RNAseq_PARP3_4d-astro_txt.txt

data_processing:
Cutadapt 1.10 (-- adapter AGATCGGAAGAGCACACGTCTGAACTCAGTCAC--quality-cutoff 20,20--anywhere"A(100)--minimum-length 40) was used for read preprocessing: adapter, poly-A and low quality (Phred quality score below 20) bases trimming, removal of readers shorter than 40 bp after trimming. Reads mapping to spike and rDNA sequences were also discarded.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR (1) version 2.5.3a (--twopassMode Basic). (1) A. Dobin et al. Bioinformatics 29(1) 15-21. 2013.
Gene expression was quantified using htseq-count (2) release 0.6.1p1 (--mode union --minaqual 10) and gene annotations from Ensembl release 92. (2) S. Anders et al. Bioinformatics 31(2) 166-169. 2015.
Statistical analysis was performed using R and DESeq2.1.16.1 Bioconductor library (3). (3) M. Lowe et al. Genome Biol. 15(12) 550. 2014.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNAseq_PARP3_4d-astro.txt: Tab-delimited text file

source_name: 4 days astrocytes

growth_protocol: Viable single NPSC cells were seeded at a density of 3,5.10e6 cells.10 ml-1 (P100 dishes) or 6.10e5 cells.3 ml-1 (6 well/plates) in plates coated with Poly-L-Lysine and Laminin. Differentiation was induced with Dulbecco’s Modified Eagle’s Medium (DMEM) High Glucose 4.5 g l-1 supplemented with 1% N2 supplement (Invitrogen), 2 mM GlutaMAX (Invitrogen), 1% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin.

extract_protocol:
Total RNA from cells was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions.

tag: strain/background

tag: genotype/variation

value: NPSC differentiated to astrocytes d4


title: 12h-low-TNFa treatment on pretreatment, RNAseq, rep2

source_name: 12h-low-TNFa treatment on pretreated cells

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days, and add 0.4 ng/mL TNF-alpha 12 hours


title: Mt01 AVI

value: Type 1 Diabetes

value: monocyte-derived dendritic cells

value: Liraglutide


title: non-treated WT RNA-seq, rep1


title: 12h-low-TNFa treatment on pretreatment, RNAseq, rep1


title: PI2-sg7-Rep3

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation
targeted amplicon sequencing; two step PCR


title: PARP3KO_ASTRO_1


title: PI2-sg7-Rep2


title: PI2-sg7-Rep1


title: Mt01 Control

value: PBS


title: 12d-TNFa treatment+withdraw-10d for high-low comparison, RNA-seq, rep1

source_name: 12d-TNFa treated HEK 293 cells+withdraw-10d

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days


title: 12h-high-TNFa treatment on pretreatment, RNAseq, rep1


title: PARP3WT_ASTRO_2


title: PARP3KO_ASTRO_2


title: Mt01 Lipos

value: Subject 01

value: PSAB-liposomes


title: 12d-TNFa treatment+withdraw-10d for high-low comparison, RNA-seq, rep2

value: HEK 293 transfected with reporter construct


title: Benign Tissue, Biological Replicate 9

type: RNA

city: Kalyani

first: Bishnupriya

last: Chhatriya

state: West Bengal

address: PO NSS

country: India

institute: National Institute of Biomedical Genomics

description: Gene expression data from adjascent normal pancreatic headmass tissue of Pancreatic  Adenocarcinoma patient.

hyb_protocol: Biotinylated RNA were hybridized onto Affymetrix HTA 2.0 Arrays  for overnight in the hybridization oven and then the array chips were  washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Data were processed using R bioconductor packages 'oligo' and 'affyPLM' and normalized using the invariant set method.

label: Biotin

source_name: Pancreatic Headmass Tissue

label_protocol: RNA were biotinylated according to standard Affymetrix protocol.

extract_protocol: Total RNA was isolated usingAllPrep DNA/RNA/miRNA Universal kit t from QIAGEN .

treatment_protocol: After excision of tissue they were put in RNA Later at 4 °C overnight and then frozen in -80 °C.

tag: age

tag: Sex

value: Female

value: pancreatic headmass

value: Adjacent Normal

tag: patient diagnosis

value: Pancreatic  Adenocarcinoma


title: Benign Tissue, Biological Replicate 15

description: Gene expression data from pancreatic headmass tissue ofChronic Pancreatitis patient.

value: Chronic Pancreatitis


title: PI3-sg7-Rep1

value: HEK

tag: treatment method

value: Lipofection

tag: treatment type


title: Benign Tissue, Biological Replicate 14

value: Male


title: Malignant Tissue, Biological Replicate 11

description: Gene expression data from  pancreatic headmass tissue of Pancreatic  Adenocarcinoma patient.

value: Tumor


title: Benign Tissue, Biological Replicate 8


title: PI1-sg7-Rep3


title: PARP3WT_ASTRO_3

value: NPSC differentiated to astrocytes d4


title: PARP3WT_ASTRO_1


title: PI1-sg7-Rep2


title: 12h-low-TNFa treatment RNAseq, rep2

source_name: 12h-low-TNFa treated HEK 293 cells

value: TNF-alpha treatment 12 hours, 0.4 ng/mL


title: 9h-TNFa treated WT RNA-seq, rep2

value: TNF-alpha treatment 9 hours


title: PI1-sg7-Rep1


title: 12h-high-TNFa treatment RNAseq, rep1

source_name: 12h-high-TNFa treated HEK 293 cells

value: TNF-alpha treatment 12 hours, 50 ng/mL


title: Het_120h_Sample_3

description: 120 hour Fused Heterokaryons

data_processing:
Alignment of the FASTQ Files were performed using bowtie2 (version 2.2.6) aligner. Alignment was done using using  --no-mixed --no-discordant flags to eliminate ambiguous read pairs and only counting reads where both pairs were mapped. PE data was directly converted to sorted BAM format using the samtools API.
BAM files were converted into EntrezGene count files using the summarizeOverlaps function in the GenomicAlignments package (v 1.8.4) using "union" mode, dropping reads mapped to multiple features. Reads were counted using the MM10 and HG19 genomes downloaded from the UCSD Genome Browser database.
Multi-mapping reads were corrected in 2 steps. First, reads that mapped to both genomes but aligned within a gene boundary for only one genome were assigned to aligned gene boundary and genome. Second, reads that mapped gene boundaries for both human and mouse genomes were evenly split between both genes. For example if a read mapped to Human Gene A that already had 4 reads mapped to it, and Mouse Gene B that already had 6 reads assigned to it, then Gene A would receive 0.4 reads, and Gene B would receive 0.6 reads.   Additional details for the correctly algorithm can be found in the associated publication.  Uploaded count files have been aligned, mapped, and corrected using these methods.
Genome_build: Human (HG19) and Mouse (MM10) genomes were downloaded from the Illumina igenome database (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) for indexing and aligment with bowtie2. For generation of count files, MM10 and HG19 genomes were downloaded from the USCD Genome Browser database (http://hgdownload.soe.ucsc.edu/downloads.html)
Supplementary_files_format_and_content: Count Files contain the corrected count values for Human and Mouse genes.

organism:
Homo sapiens
Mus musculus

source_name: Tcf3-/- Mouse ESC + Human B cell line

growth_protocol: Tcf3-/- mouse embryonic stem cells were cultured in DMEM media supplemented with 10% foetal bovineserum and murine LIF. Human B lymphocytes were cultured in RPMI media supplemented with 20% foetal bovine serum

extract_protocol:
The cells were processed using the Qiagen RNA extraction kit for isolating the RNA
RNA Samples isolated from the heterokaryons were further processed to generate sequencing libraries using a Truseq RNA library Prep Kit.
The libraries were then analyzed on an Illumina HiSeq 2000 sequencer using 100 bp paired-end sequencing.

treatment_protocol: Tc3-/- mouse embryonic stem cells were labeled with Vybrant DiD and Human B lymphocytes were labeled with Vybrant DiO. Both labeled cells were mixed and treated withpolyethylene glycol (PEG) at 37 deg for a maximum period of 2.5 mins. Cells were then resuspended and washed with DMEM and plated in DMEM media supplemented with 10% foetal bovine serum and mouse LIF. Finally at specific timepoints the cells labeled with both dyes were sorted by flow cytometry for RNA extraction.

value: Tcf3-/- Mouse ESC + Human B cell line

tag: strain


title: MUT3

value: 18 weeks


title: 12h-high-TNFa treatment RNAseq, rep2


title: 12h-low-TNFa treatment RNAseq, rep1


title: ABEmax7-10-sg7-Rep3


title: Benign Tissue, Biological Replicate 6

tag: disease state


title: non-treated control RNA-seq for high-low comparison, rep2

source_name: non-treated HEK 293

value: no treatment


title: Malignant Tissue, Biological Replicate 10


title: ABEmax7-10-sg7-Rep2


title: Benign Tissue, Biological Replicate 7


title: Benign Tissue, Biological Replicate 13


title: non-treated control RNA-seq for high-low comparison, rep1

value: HEK 293 transfected with reporter construct


title: ABEmax7-10-sg7-Rep1


title: 12d-TNFa treatment+withdraw-10d, RNA-seq, rep2

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days


title: 12d-TNFa treatment+withdraw-10d+12h TNFa, RNA-seq, rep2

source_name: 12d-TNFa treated HEK 293 cells+withdraw-10d+12h-TNFa

value: TNF-alpha treatment 12 days, then withdraw to recover 10 days, and add TNF-alpha 12 hours


title: Het_48hr_Sample_1

description: 48 hour Fused Heterokaryons


title: 12d-TNFa treatment+withdraw-10d+12h TNFa, RNA-seq, rep1


title: Het_12hr_Sample_3

description: 12 hour Fused Heterokaryons


title: Het_120h_Sample_2

description: 120 hour Fused Heterokaryons


title: Malignant Tissue, Biological Replicate 8

value: pancreatic headmass


title: PI3-sg4-Rep3


title: Het_12hr_Sample_2

description: 12 hour Fused Heterokaryons


title: Het_120h_Sample_1

description: 120 hour Fused Heterokaryons


title: PI3-sg4


title: Benign Tissue, Biological Replicate 12


title: PI3-sg4-Rep1


title: Het_48hr_Sample_2

description: 48 hour Fused Heterokaryons


title: Malignant Tissue, Biological Replicate 7

value: Female

value: Pancreatic  Adenocarcinoma


title: 12d-TNFa treatment RNAseq, rep2

source_name: 12d-TNFa treated HEK 293 cells

value: TNF-alpha treatment 12 day


title: Malignant Tissue, Biological Replicate 6


title: Benign Tissue, Biological Replicate 11

value: Chronic Pancreatitis


title: Het_48hr_Sample_3

description: 48 hour Fused Heterokaryons


title: Het_4hr_Sample_3

description: 4 hour Fused Heterokaryons


title: PI3-sg4-Rep2

value: HEK

value: Lipofection


title: Het_12hr_Sample_1

description: 12 hour Fused Heterokaryons


title: 12d-TNFa treatment RNAseq, rep1


title: Benign Tissue, Biological Replicate 10

value: Male


title: PI2-sg4-Rep1


title: PI2-sg4-Rep2


title: Het_4hr_Sample_1

description: 4 hour Fused Heterokaryons


title: Het_4hr_Sample_2

description: 4 hour Fused Heterokaryons


title: 12d-TNFa treatment+withdraw-10d, RNA-seq, rep1


title: PI2-sg4


title: 12h-TNFa treatment RNAseq, rep1

source_name: 12h-TNFa treated HEK 293 cells

value: TNF-alpha treatment 12 hours


title: Malignant Tissue, Biological Replicate 5

value: Tumor


title: Malignant Tissue, Biological Replicate 9


title: PI2-sg4-Rep3


title: non-treated control RNA-seq, rep2


title: non-treated control RNA-seq, rep1


title: 12h-TNFa treatment RNAseq, rep2


title: Mt08 Lipos

source_name: peripheral blood

tag: individual id

value: Subject 08

value: Type 1 Diabetes

value: monocyte-derived dendritic cells

tag: treatment (cultured with)

value: PSAB-liposomes


title: Malignant Tissue, Biological Replicate 4


title: Benign Tissue, Biological Replicate 5

value: Adjacent Normal


title: eS7_4KR.4hr.RNA-seq_rep2

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

country: Japan

institute: The University of Tokyo,

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to Genome
Read quantitation using custom scripts
Genome_build: sacCer3
Supplementary_files_format_and_content: text files contain following columns: 1.gene name 2.length (codon) 3.reads counts

organism: Saccharomyces cerevisiae

extract_protocol:
RNA extraction
The lysate was treated with RNase I and then subjected to ultracentrifugation for ribosome profiling. Total RNA was extracted by TRIzol reagent from the lysate (RNA-seq) or ribosome pellet (Ribosome profiling).
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 . RNA-seq libraries were generated from rRNA-depleted total RNA using an Illumina TruSeq stranded total RNA kit.

value: Tm treatment for 4hr

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPS7a::HisMX6 RPS7b::natNT2 pRS315-RPS7a-4KR-3HA

tag: cell line


title: X136_S25: LNCaP-C4-2_CTL_OE_rep2

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Illumina adapters were removed using BBDuk and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (hg38.p12, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Differential gene expression was calculated using the voom function in limma
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing STAR gene count values

growth_protocol: LNCaP-C4-2 cells were grown in RPMI with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol:
RNA was extracted using a RNeasy Plus Mini Kit (Qiagen). RNA quality was verified using a High Sensitivity ScreenTape Assay on the Tape Station 4200 (Agilent Technologies) and measured with a Tecan Plate Reader (Thermo Fisher Scientific).
Library construction was performed using the Universal Plus mRNA Library Kit (NuGen Technologies), and sequencing was performed on the NovaSeq 6000 instrument (Illumina) using paired-end sequencing (2x150 bp) by the University of Colorado Cancer Center Genomics and Microarray Core.

treatment_protocol: For the knockdown (KD) treatment, cells were transduced with control (Scrambled) or  CPT1A-targeting shRNA lentivirus and selected with 1 ug/ml Puromycin. For the overexpression (OE), cells were transduced with control (empty vecotr) or CPT1A cDNA  lentivirus and selected with 5 ug/ml Blasticin.

value: Prostate cancer


title: X140_S28: LNCaP-C4-2_CPT1A_OE_rep3


title: X139_S27: LNCaP-C4-2_CPT1A_OE_rep2


title: X138_S26: LNCaP-C4-2_CPT1A_OE_rep1


title: PI1-sg4

data_processing:
Library strategy: DNA-seq
We directly analzed the fastq files using an online tool CRISPRESSO2.  We therefore do not have any additional processed data.


title: PI1-sg4-Rep1


title: X135_S24: LNCaP-C4-2_CTL_OE_rep1


title: eS7_4KR.4hr.RNA-seq_rep1


title: Benign Tissue, Biological Replicate 3

value: pancreatic headmass


title: Malignant Tissue, Biological Replicate 2

value: Pancreatic  Adenocarcinoma


title: Benign Tissue, Biological Replicate 4


title: X134_S23: LNCaP-C4-2_CPT1A_KD_rep3


title: ABEmax7-10-sg4-Rep3


title: Malignant Tissue, Biological Replicate 1

value: Female


title: ABEmax7-10-sg4-Rep2


title: Benign Tissue, Biological Replicate 2


title: PI1-sg4-Rep3


title: eS7_WT.4hr.RNA-seq_rep2

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPS7a::HisMX6 RPS7b::natNT2 pRS315-RPS7a-3HA


title: eS7_4KR.0hr.RNA-seq_rep1


title: X133_S22: LNCaP-C4-2_CPT1A_KD_rep2


title: PI1-sg4-Rep2

value: HEK


title: Benign Tissue, Biological Replicate 1


title: ABEmax7-10-sg4-Rep1

value: Lipofection


title: eS7_4KR.0hr.RNA-seq_rep2


title: X132_S21: LNCaP-C4-2_CPT1A_KD_rep1


title: ABEdHNH7-10-sg4-Rep1


title: Malignant Tissue, Biological Replicate 3


title: eS7_WT.4hr.RNA-seq_rep1


title: 170118A-E-4-1

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

description: mRNA from single cells

data_processing:
Transcripts from human donors were mapped to the reference genome (GRCh38) using Cell Ranger Version 3.0.2
Transcripts from mice were mapped to the reference genome (GRCm38/mm10) using Cell Ranger Version 2.0.1
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Processed files were analyzed with Seurat V3.1.0, Monocle V2.10.1, scEpath V1 and Velocyto.R V0.6.
Genome_build: mm10
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Scrotal skin epidermis

growth_protocol: N/A. Primary cells were used in this study.

extract_protocol:
Human: Human EMPD (Patient ID; n=1) and normal skin (Patient ID; n=1; normal skin constitutes site adjacent to EMPD lesion). Samples were surgically excised and placed in tissue storage solution (MACS). Samples were processed for single cell isolation within 10 hours post-surgery. Excess subcutaneous adipose and dermal tissues were excised. Samples were cut into pieces with a maximum diameter of 4 mm. Skin specimens were then washed twice with cold 1X PBS. Single cells were isolated using the human epidermis isolation kit (MACS) as per manufacturer’s instructions with minor modifications. Mouse: Skin epidermal cells were collected from DTG (n=1) and control (n=1) newborn mice (post-natal day 0.5) 5 days after Doxycycline treatment. Mice were euthanized, and consecutively immersed in 70% ethanol and cold 1X PBS twice for 3 minutes. Fore and hind limbs and tail were cut off and skin was peeled along the ventral midline axis with blunt tweezers. Subcutaneous adipose tissue was micro-dissected. 12 mm skin biopsies were laid on EpiLife CF basal media (STEM CELL) droplets (300 μL) on a 12-well plate with skin dermis side down. 2 ml (2.5 U/mL) Dispase solution (STEM CELL)  was added to skin and incubated at 4℃ for 12 hrs. Epidermis was separated from dermis with two sharp tweezers and placed on Accutase (ThermoFisher) droplets (500 μL) for 30 min (dermis side down) at RT to create single cell suspensions.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry (mouse samples) and Single Cell 3' v3 chemistry (human samples). Cell capture, library preparation, quality control, and sequencing was performed at Beijing CapitalBio Technology (Beijing, China).
Single Cell 3’ v2 chemistry (mouse samples) - 10X Genomics

value: EMPD scrotal skin

value: Adult - 58 years old


title: eS7_WT.0hr.RNA-seq_rep2


title: PI3-sg1-Rep3

source_name: HEK cells


title: X129_S19: LNCaP-C4-2_CTL_KD_rep1


title: X130_S20: LNCaP-C4-2_CTL_KD_rep2


title: WT.4hr.RNA-seq

value: MATa ade2 his3 leu2 trp1 ura3 can1


title: 170118A-E-3-1

description: mRNA from single cells

treatment_protocol: N/A. Primary cells were used in this study.


title: PI2-sg1-Rep3


title: SEM_IFNg_6hr_R3

city: Cambridge

first: Tony

last: D'Alessio

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

data_processing:
FASTQ files were created using bcl2fastq version 2.17.1.
Transcript and gene abundances from RNAseq libraries were estimated using salmon (Patro et al., Nature Methods 2017) version 0.8.2, run with default parameters plus --seqBias, --gcBias, and –useVBOpt, against the Gencode v25 transcriptome.
TMM scaling of the TPM values was performed as described in Robinson and Oshlack (Genome Biology, 2010).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. Last 6 columns contain gene metadata.
Supplementary_files_format_and_content: Matrix table with TPM (transripts per million) counts for every gene and every sample. Last 6 columns contain gene metadata.
Supplementary_files_format_and_content: Matrix table with trimmed mean of M values (TMM)-scaled TPM counts for every gene and every sample. Last 6 columns contain gene metadata.

source_name: cancer cell line

growth_protocol: MOLM13, SEM, HCC827 cells were cultured in RPMI with 10% FBS. Cells were expanded and maintained in 0.5-1 million cells/ml. For each cell line, 10 million cells were collected for IFNg treatment

extract_protocol:
The total RNA for each sample was extracted using the PureLink™ RNA Mini Kit (Invitrogen Catalog #12183018A). The RNA quality was assessed using the Bioanalyzer 2100 (Agilent) to ensure RIN scores for all samples were above 9.0. RNA samples were diluted to 4ng/μl for RNA sequencing.
Total RNA was quantified using the Agilent RNA 6000 Nano Kit (catalog number 5067-1511) on the Agilent 2100 BioAnalyzer. Two hundred nanograms of high purity RNA (RNA Integrity Number 7.0 or greater) was used as input to the Illumina TruSeq Stranded mRNA Library Prep Kit, High Throughput (catalog number RS-122-2103), and the sample libraries were generated per manufacturer’s specifications on the Hamilton STAR robotics platform. The PCR amplified RNA-Seq library products were then quantified using the Advanced Analytical Fragment Analyzer Standard Sensitivity NGS Fragment Analysis Kit (catalog number DNF-473).

treatment_protocol: MOLM13, SEM, HCC827 cells were treated with 100ng/ml human IFNg (Peprotech Catalog #300-02). Cell lysates were collected at 0hr, 6hrs, 24hrs post IFNg treatment. Samples were prepared in triplicates.

value: SEM

value: 100 ng/ml interferon gamma

tag: time

value: 6 hours


title: 170118A-E-2-1

description: mRNA from single cells

tag: tissue


title: 170118A-E-1-1

description: mRNA from single cells


title: SEM_IFNg_6hr_R2


title: WT.1hr.RNA-seq

value: Tm treatment for 1hr


title: PI2-sg1-Rep2


title: SEM_IFNg_6hr_R1


title: PI3-sg1-Rep1


title: 170118A-N-4-1

description: mRNA from single cells

value: Normal scrotal skin


title: Untreated P. falciparum NF54 gametocytes

city: Pretoria

first: LynMarie

last: Birkholtz

state: Gauteng

address: c/o Lunnon Road and Heroldt Street, Hatifeld

department: Biochemistry

country: South Africa

institute: University of Pretoria

description: NF54 gametocytes without drug perturbation (control corresponding to ML324 treated gametocytes)

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Slides were scanned on an Agilent G2600D Microarray Scanner (5 µm resolution) at wavelengths of 532 nm (Cy3) and 633 nm (Cy5), output images were quantified and signal intensities extracted with Agilent Feature Extraction Software (v 11.5.1.1) using the GE2_1100_Jul11_no_spikein protocol.

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and log2(Cy5/Cy3) (log2-transformed expression values) reported.

organism: Plasmodium falciparum

source_name: Untreated RNA

growth_protocol: Reader, J., Botha, M. E., Theron, A., Lauterbach, S.B., Rossouw, C., Engelbrecht, D., Wepener, M., Smit, A., Leroy, D., Mancama, D., Coetzer, T.L. and Birkholtz, LM. Nowhere to hide: interrogating different metabolic parameters of Plasmodium falciparum gametocytes in a transmission blocking drug discovery pipeline towards malaria elimination. Malar. J. 14:213 (2015). P. falciparum (NF54) asexual parasites [maintained in human erythrocytes (5% haematocrit) in complete culture medium (RPMI 1640 (Sigma-Aldrich) supplemented with 25 mM HEPES, 20 mM glucose, 200 μM hypoxanthine, 0.2% (w/v) sodium bicarbonate, 24 μg/ml gentamycin and 0.5% (w/v) AlbuMAX II) at 37°C and under hypoxic conditions (90% N2, 5% O2, and 5% CO2)] were synchronised (>95% ring stage parasites) using 5% D-sorbitol for two consecutive replication cycles and were then subjected to glucose starvation and a reduced haematocrit (4%) to induce gametocyte commitment. N-acetylglucosamine (50 mM) supplemented media was changed daily from day 1 of development to remove residual asexual parasites.

treatment_protocol: Gametocytes were treated with 5 µM ML324 (Sigma-Aldrich)and incubated at  37˚C without agitation in parallel with untreated control gametocyte samples for 24 h. Gametocytes (1-3% gametocytaemia)  were then isolated from host erythrocytes using 0.01% (w/v) saponin, washed three times with 1x PBS and stored at -80˚C for further use.

tag: time after treatment

value: 24 hours (No treatment)

source_name: 3D7 mixed asexual parasites, treated and untreated NF54 gametocytes Reference Pool


title: WT.0hr.RNA-seq_rep2


title: PI3-sg1-Rep2

last: Rothgangl

address: Winterthurerstrasse, 190

institute: UZH Zurich


title: ML324-treated P. falciparum NF54 gametocytes

description: NF54 gametocytes treated with 5 µM ML324 and sampled 24 h after treatment

source_name: ML324 treated RNA

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

value: 24 hours


title: PI2-sg1-Rep1


title: 170118A-N-3-1

description: mRNA from single cells


title: SEM_IFNg_24hr_R3

tag: treatment


title: WT.0hr.RNA-seq_rep1


title: PI1-sg1-Rep3


title: 170118A-N-2-1

description: mRNA from single cells


title: WT.2hr.RNA-seq

value: Tm treatment for 2hr


title: eS7_4KR.4hr.Ribo-seq_rep2

description: Ribosome Profiling

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to Genome
Read quantitation using custom scripts
Genome_build: sacCer3
Supplementary_files_format_and_content: text files contain following columns: 1.gene name 2.length (codon) 3.reads counts

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
The lysate was treated with RNase I and then subjected to ultracentrifugation for ribosome profiling. Total RNA was extracted by TRIzol reagent from the lysate (RNA-seq) or ribosome pellet (Ribosome profiling).
Ribosome profiling libraries were generated as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112-129 . RNA-seq libraries were generated from rRNA-depleted total RNA using an Illumina TruSeq stranded total RNA kit.

value: Tm treatment for 4hr

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPS7a::HisMX6 RPS7b::natNT2 pRS315-RPS7a-4KR-3HA


title: SEM_IFNg_24hr_R2


title: PI1-sg1-Rep2


title: SEM_IFNg_24hr_R1


title: 170118A-N-1-1

description: mRNA from single cells


title: PI1-sg1-Rep1


title: Prog_treated_with_BAZ2B: Lineage-CD34+CD38+ progenitors treated with BAZ2B for 14 days

data_processing:
The sequenced reads from the Illumina sequencer were processed through the Cell Ranger (v 2.0.0) pipeline. Note that one raw data file was a resequencing run that pooled the Luciferase and BAZ2B libraries. It was demultiplexed and added to those libraries for analysis.
Demultiplexed FASTQ files (Cell Ranger v 2.0.0).
BAM files (Cell Ranger v 2.0.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: The cellranger count program also generated the HDF5 gene barcode matrix files that contain only the detected barcodes. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

extract_protocol:
Single cells were sorted in a BD Influx cytometer and were pelleted by centrifugation followed by resuspension in DMEM at approximately 500cells/µl. Cell viability and concentration was verified by Countess cell counter.
Each sample was loaded into one well of a Chromium chip (10X Genomics, #120236), following manufacturer’s instructions, and aiming for a recovery of 5,000 cells per sample. Library construction was carried out according to the manufacturer’s instructions and were sequenced on Illumina Hiseq 2000.

value: Umbilical cord blood

tag: surface markers

value: Lineage-GFP+


title: ABEmax7-10-sg1-Rep3

value: HEK


title: eS7_4KR.0hr.Ribo-seq_rep2

description: Ribosome Profiling


title: eS7_4KR.0hr.Ribo-seq_rep1

description: Ribosome Profiling


title: SEM_IFNg_0hr_R1

value: 0 hours


title: Prog_treated_with_Luciferase: Lineage-CD34+CD38+ progenitors treated with Luciferase for 14 days


title: ABEmax7-10-sg1-Rep2

value: Lipofection


title: CD34pos_treated_with_BAZ2B: CD34+ progenitors treated with BAZ2B for 14 days

data_processing:
The sequenced reads from the Illumina sequencer, were processed through the Cell Ranger (v 2.0.0) pipeline.
Demultiplexed FASTQ files (CellRanger v 2.0.0)
BAM files (Cell Ranger v 2.0.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: The cellranger count program also generated the HDF5  gene barcode matrix files that contain only the detected barcodes. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

growth_protocol: Human CD34+ cells were cultured in serum-free enhanced media supplemented with two different formulations of recombinant human cytokines, (1) Stimulation media – contains SCF 300 ng/ml, FLT3 300 ng/ml, TPO 100 ng/ml, IL3 60 ng/ml (2) Maintenance media - SCF 100 ng/ml, FLT3 100 ng/ml, TPO 100 ng/ml, IL3 20 ng/ml, IL6 20 ng/ml. For experiments using the entire fraction of CD34+ cells, the cells were incubated in the stimulation media for 24 hours at 37 degrees C.

extract_protocol:
Single cells were sorted in a BD Influx cytometer and  were pelleted by centrifugation followed by resuspension in DMEM at approximately 500cells/µl. Cell viability and concentration was verified.
Each sample was loaded into one well of a Chromium chip (10X Genomics, #120236), following manufacturer’s instructions, and aiming for a recovery of 5,000 cells per sample. Library construction was carried out according to the manufacturer’s instructions and were sequenced on Illumina Hiseq 2000.


title: eS7_WT.4hr.Ribo-seq_rep2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1 RPS7a::HisMX6 RPS7b::natNT2 pRS315-RPS7a-3HA


title: ABEmax7-10-sg1-Rep1


title: eS7_WT.4hr.Ribo-seq_rep1

description: Ribosome Profiling


title: MOLM13_IFNg_6hr_R3


title: CD34pos_treated_with_Luciferase: CD34+ progenitors treated with Luciferase for 14 days


title: MOLM13_IFNg_6hr_R2


title: SLp_3_mRNA

city: Oslo

first: Magnus

middle: D.

last: Vigeland

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

description: processed data file: counts_gencode.M16_LEFT.txt

data_processing:
Trimming of fastq files with Trim Galore! (v0.4.3; default parameters).
RRBS alignment to mm10, by Bismark v0.20, powered by bowtie2.
RRBS analysis of methylated/unmethylated read counts, by R package edgeR.
RNA-Seq alignment and feature counts, by R package Rsubread.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bismark coverage file: Tab-delimited file with one row for each covered cytosine position in the experiment, and the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
Supplementary_files_format_and_content: counts_gencode.M16_LEFT.txt: Feature counts: Tab-delimited file with one row per gene. The first column has Gene ID (Ensembl), followed by one column per sample, with unnormalised counts.

source_name: Hippocampus

extract_protocol:
24 hours after status epilepticus right hippocampi were extracted and flash frozen. Tissue was thawed in homogenization buffer and homogenized on a GentleMACS dissociator (Miltenyi). Debris was removed by density gradient centrifugation, using Debris Removal Solution (Miltenyi cat.no. 130-109-398). Nuclei were resuspended in buffer and stained with anti-NeuN-Alexa Fluor488 (Millipore cat.no. MAB377X), followed by sorting on BD FACSAria (BD Biosciences). RNA was extracted from NeuN positive nuclei, following procedures E and F.I in the mirVana miRNA Isolation Kit protocol (Ambion cat. no. AM 1560). RNA was up-concentrated using the RNA Clean & Concentrator-5 kit (Zymo Research cat.no. R1015).
SMART-Seqv4 Ultra Low InputRNA Kit for Sequencing (Takara Bio cat.no. 634891) was used to amplify 1 ng mRNA from total RNA, with 10 cycles of PCR performed. The resulting cDNA was used as input in library preparation with ThruPlex DNAseq Kit (Rubicon Genomics cat.no. R400407).

value: Hippocampus

value: Sham

tag: neun

value: positive

tag: biol. repl.


title: eS7_WT.0hr.Ribo-seq_rep2

description: Ribosome Profiling