title: M8_pob3_H2BK119R_2

data_processing:
50 bp paired-end reads were aligned to the reference (Schizosaccharomyces pombe ASM294v2) using bowtie2 (version 2.2.9).
Reads were filtered by samtools with -q 2 parameter (version 1.3.1).
BAM alignments were converted to BEDPE format using bedtools2 (version 2.26.0), from which fragment coordinates were extracted.
Dyad coverages were calculated using the bed2dyad function from the tsTools R package with the width parameter 50 (version 0.1.0).
Genome_build: Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: Bigwig (bw) format. Normalized dyad coverage.

extract_protocol:
500 ml of S. pombe cells were grown overnight at 30°C to OD600 ~ 0,5. Cells were crosslinked with 0.5% formaldehyde for 20 min at RT. The crosslinking was stopped with 125 mM Glycine. Cells were spun, washed with dH2O and the pellet was resuspended in 20 ml of ice cold Preincubation solution (19.7 mM Na2HPO4, 109 mM citric acid, 40 mM EDTA, 28.6 mM b-Mercaptoethanol). The cells were incubated at 30°C with vigorous shaking for 10 min. Cells were harvested at 4000 rpm for 5 min at 4°C and the pellet was resuspended in 10 ml Sorbitol/Tris buffer (1M sorbitol, 50 mM Tris pH 7.4). 10 mg of Zymolyase 100T was added and the spheroplasts were incubated at 30°C for 30 min with vigorous shaking followed by centrifugation at 400 rpm for 5 min at 4°C. The spheroplasts were washed once with 40 ml Sorbitol/Tris buffer (ice cold, without b-Mercaptoethanol) and the pellet was resuspended in 7.5 ml of NP buffer (ice cold) with 1 mM b-Mercaptoethanol and 500 µM spermidine. Samples were split into 1 ml aliquots and various amounts of MNase (Sigma, 0.6 U/ml) were added (2,4,6,8,10 and 12 ul) and the samples were incubated at 37°C for 20 min. The reaction was stopped with 138 ul of Stop Buffer (5% SDS, 100 mM EDTA). Samples were digested with 40 ul of RNAse A (10mg/ml) at 37°C for 45 min. 50 ul of Proteinase K (20 mg/ml) was added and the samples were incubated O/N at 65°C.  360 ul of 3 M potassium acetate pH 5.5 was added to each sample, incubated on ice for 10 min and spun down at 14000 rpm, 4°C for10 min. Next, the samples were phenol/chloroform extracted and DNA was precipitated with 0.2M NaCl and Isopropanol, 1 ul of glycogen (20 mg/ml) was added as a carrier. After precipitation nucleosomal DNA was washed with 70% Ethanol, air dried and resuspended in 50 ul of TE.  Samples were loaded on a 1.5% agarose gel (Biozym ME agarose) in 1 x TAE and resolved. Mononucleosmal DNA was cut out and DNA was recovered with Freeze N’ Squeeze gel extraction columns (BioRad). DNA was precipitated with isopropanol in the presence of glycogen and the pellet was resuspended in 20 µl TE. DNA was kept at -20C until library preparation.
The libraries were prepared with 50 ng of S. pombe mononucleoosmal DNA. All enzymes, buffers and primer sets were from NEB. Shortly, first DNA was end-repaired, followed by AMPure bead purification. DNA was then dA-tailed and purified with AMPure beads. Finally the adaptor ligation was performed O/N at 16°C. The reaction was treated with USER enzyme and purified with AMPure beads. Finally, the multiplexing PCR reaction was performed with a Phiusion polymerase. Usually 8 PCR cycles were performed to avoid the library over-amplification. PCR product was purified on a native 5% polyacrylamide gel and extracted in 400 ml of Gel Extraction Buffer (300 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA) O/N at 4°C. Extracted DNA was further precipitated with isopropanol and the final library was resuspended in 15 ul of 0.1 TE. DNA was measured by Qubit DNA HS (Invitrogen) and the quality of the library was further verified by Bioanalyzer.

tag: mnase units


title: YapKO CD4 TDLNs Rep 3

status: Public on Dec 11 2019

type: SRA

city: Baltimore

first: Gregory

middle: Lee

last: Szeto

state: MD

address: 1000 Hilltop Circle, ILSB room 415

country: USA

institute: UMBC

library_source: transcriptomic

data_processing:
Pass-filter Illumina reads may undergo one or both of adaptor and quality trimming upon completion of FastQC assessment. Sequence files that show adaptor contamination of 1% or higher undergo adaptor trimming using Trimmomatic enforcing a minimum Q20 trailing quality for every read. Quality trimming uses fastx_trimmer [2] to truncate reads where the quality drops below Phred scale quality of 20 (Q20). Reads that fail to meet a minimum read length of 30 bp (or 5bp for miRNA libraries) after adaptor and quality trimming are excluded from the trimmed files and so are their mates in the case of paired-end files.
Reads were assigned to transcripts using Salmon v0.9.1 in mapping mode to mouse transcriptome index.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated file with a header line containing names of all columns. Columns appear in the following order: Name, Length, Effective Length, TPM, NumReads  Each subsequent row describes a single transcript quantification. The columns have the following interpretation.    Name — ENSEMBL transcript ID with version identifier  Length — the length of the target transcript in nucleotides.  EffectiveLength — the computed effective length of the target transcript. .  TPM — the relative abundance in units of Transcripts Per Million (TPM).   NumReads — estimate of the number of reads mapping to transcript

molecule: total RNA

organism: Mus musculus

source_name: tumor-draining inguinal lymph node

extract_protocol:
B16F10 tumors and lymph nodes from wild-type or CD4Cre Yap-floxed C57BL/6J mice were mechanically and enzymatically dissociated, and cells stained for flow sorting. Live, purified CD4+ T cells, CD8+ T cells or CD45+ CD4- CD8- cells were sorted directly into TRIzol LS reagent. RNA was purified by Qiagen miRNeasy kit.
Libraries were prepared using Takara SMART-Seq® v4 Ultra® Low Input RNA Kit following manufacturer's protocol.

tag: cell type

value: CD4+ T cells

tag: strain

tag: genotype

value: CD4Cre Yap flox


title: Rod-P14-1

city: Bethesda

first: Koray Dogan

last: Kaya

address: 6 CENTER DR

department: NEI

institute: NIH

data_processing:
Paired end fastq files and single end fastq files of Rod samples from GSE74660 were aligned to protein coding cDNA fasta file annotated by Ensembl version 87 by using kallisto
Thw two types of data were summarized and normalized together by tximport

source_name: Isolated rods

growth_protocol: MEFs were grown in IMR90 medium and CiPC reprogramming was performed in photoreceptor induction medium

extract_protocol: Cells were sorted by promoter reporter expression and RNA was prepared by quick RNA micro kit from zymo research (R1050). Each sample contains 80ng of total RNA.

treatment_protocol: five chemical treatment for 11 days in induction medium

tag: tissue

value: Isolated rods

value: Strain (Nrl-GFP)

tag: developmental stage

value: Postnatal day 14


title: YapKO CD4 TDLNs Rep 2


title: M8_pob3_H2BK119R_1

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

library_source: genomic

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: whole cell


title: Rod-P10-3

value: Postnatal day 10


title: YapKO CD4 TDLNs Rep 1


title: WT CD4 TDLNs Rep 3

value: WT


title: M8_pob3_2


title: Rod-P10-2


title: M8_pob3_1


title: M8_H2BK119R_2


title: M8_WT_1


title: Rod-P10-1


title: Rod-P6-3

value: Postnatal day 6


title: Rod-P14-3


title: M6_pob3_H2BK119R_2


title: M8_H2BK119R_1


title: WT CD4 TDLNs Rep 2


title: Rod-P6-2


title: WT CD4 TDLNs Rep 1


title: M6_pob3_H2BK119R_1


title: M6_pob3_2


title: M6_WT_2


title: YapKO CD8 TDLNs Rep 4

value: CD8+ T cells


title: Rod-P10-4


title: Rod-P6-1


title: 43_L1.N707

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

data_processing:
Raw read data was aligned against mouse transcriptome (MouseEnsembl release 61) using Bowtie2 (Langmead and Salzberg, 2012). Splice junctions were defined as available in Ensembl v75. Read mappings were then mapped to genes and transcripts based on the transcript models annotated in Ensembl v75 using in-house tools and, again using in-house software, RPKM values were computed as described previously (Mortazavi et al., 2008).
Genome_build: MouseEnsembl release 61
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: MMTV-PyMT mammary tumors

extract_protocol:
Cell sorting was performed using FACS Aria II apparatus (BD). Each cell population (n=4) was isolated from an independent tumor. Typically, 2x104 to 2x105 cells were obtained for each cell population. Sorted cell populations were immediately homogenized in 700 µl Qiazol reagent (Qiagen). 140 µl of chloroform was added to the homogenate and the mixture centrifuged at 16,000 x g for 5 min at 4°C in Phase Lock Tubes (Qiagen). RNA was subsequently extracted from the aqueous phase using the RNeasy Micro kit (Qiagen) according to manufacturer’s instructions. Genomic DNA was removed using the RNase free DNase set (Qiagen) during the extraction. RNA was quality controlled on Agilent Eukaryote Total RNA pico chips (Agilent Technologies). High quality RNA (RIN >7) was obtained for all samples. SMARTer ultra low RNA kit for Illumina sequencing (Clontech) was used to prepare and amplify cDNA from 520 pg of total RNA according to manufacturer’s instructions.
Then, 1 ng of amplified cDNA was subjected to Nextera XT library preparation (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantified using the Kapa Library Quantification kit (Kapa Biosystems) and quality controlled by capillary electrophoresis on a Bioanalyzer using High Sensitivity chips (Agilent Technologies). Libraries were sequenced on a HiSeq2500 sequencer (Illumina) for 2 x 50 cycles using version 4 cluster generation kits and version 4 sequencing reagents (Illumina).

treatment_protocol: When tumors reached a size of 300 mm3, mice were injected i.p with the following moAbs: mouse IgG1 (clone MOPC-21, 500 μg) + rat IgG2a (clone 2A3, 100 μg), designated as “IgG”; or anti-VEGFA/ANGPT2 (A2V, 500 μg) + rat IgG2a (clone 2A3, 100 μg), designated “A2V”.  Five days later, mice were euthanized and tumors harvested and prepared for fluorescence-activated cell sorting (FACS).

value: CD8+ cells

tag: treatment


title: M6_H2BK119R_2


title: Rod-P4-2

value: Postnatal day 4


title: M8_WT_2


title: YapKO CD8 TDLNs Rep 3


title: M6_H2BK119R_1


title: M4_pob3_H2BK119R_2


title: YapKO CD8 TDLNs Rep 2


title: Rod-P4-1


title: Rod-P2-2

value: Postnatal day 2


title: YapKO CD8 TDLNs Rep 1


title: M4_pob3_2


title: Rod-P2-1


title: M4_pob3_1


title: M4_WT_2


title: M4_pob3_H2BK119R_1


title: WT CD8 TDLNs Rep 3


title: M6_pob3_1


title: M4_WT_1


title: WT CD8 TDLNs Rep 2


title: M4_H2BK119R_1


title: M2_pob3_H2BK119R_2


title: WT CD8 TDLNs Rep 1


title: M6_WT_1


title: M2_pob3_2


title: WT CD8 TDLNs Rep 4


title: M2_pob3_1


title: M2_WT_2


title: M2_pob3_H2BK119R_1


title: S8_Regnase1_null2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
The Cell Ranger 1.3 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

source_name: sgRNA transduced OT-I cells from the B16-Ova melanoma-bearing mice

extract_protocol:
CD8+ T cells were sorted from sgRNA transduced OT-I cells from the B16-Ova melanoma tumor
Single-cell suspensions were loaded onto the Chromium Controller according to their respective cell counts to generate 6000 single cell GEMs (gel beads in emulsion) per sample. Libraries were prepared using the Chromium Single Cell 3’ v2 Library and Gel Bead Kit (10x Genomics)

tag: strain background

value: sgRNA transduced OT-I cells

tag: genotype/variation


title: M2_WT_1


title: S7_Regnase1_null1


title: M2_H2BK119R_2


title: S6_WT2

value: wild type


title: M2_H2BK119R_1


title: S5_WT1


title: RNA_pob3_H2BK119R_2

data_processing:
50 bp single reads were aligned to the reference genome (Schizosaccharomyces pombe ASM294v2) using STAR (version 2.5.3a).
Strand separated coverage vectors were generated from the BAM files and normalized to the total coverage using Bioconductor packages.
Genome_build: Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: Bigwig (bw) format. Strand separated normalized coverage.

extract_protocol:
50 ml of yeast culture at OD600 ~0.5-0.8 was spun down at RT and the pellet frozen in liquid nitrogen. Cells were thawed on ice and resuspended in 1 ml of TRIzol. 250 ul of zirconia beads were added and cells wee broken with Precyllis 24 (Peqlab) for 3x30 s with 5 min rest on ice. The extract was spun down at 13500 rpm at 4°C for 10 min. The cleared lysate was extracted twice with chloroform and spun at 13500 rpm at 4°C for 10 min. The aqueous phase was taken and RNA was precipitated with isopropanol. The pellet was washed twice with 75% EtOH, air dried and resuspended in 50 ml of RNAse free dH20. The RNA concentration and purity was determined by Nano-drop.
RNA for RNA-seq was prepared as described above. 1 mg of RNA was treated with NEBNext®Poly(A) mRNA Magnetic Isolation Module to enrich for poly-adenylated transcripts. The libraries were prepared with NEBNext®Ultra™Directional RNA Library Prep Kit for Illumina® according to the manual instructions.


title: RNA_pob3_H2BK119R_1


title: M4_H2BK119R_2


title: RNA_pob3_1


title: RNA_pob3_2


title: RNA_WT_2


title: BatfReg1dKO4 [JWA22]

data_processing:
Adapter sequences were removed using trimmomatic v.0.36
and aligned them to the mouse genome mm9 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM37_um.fa) using the Burrows–Wheeler algorithm32 (version 0.7.16, default parameter)
duplicated reads were then marked with Picard (version 2.9.4) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.1, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

value: B16-Ova melanoma-bearing mice


title: RNA_WT_1


title: BatfReg1dKO3 [JWA21]


title: BatfReg1dKO2 [JWA20]


title: RNA_H2BK119R_1


title: RNA_H2BK119R_2


title: BatfsKO2 [JWA18]

value: BatfsKO


title: BatfReg1dKO1 [JWA19]


title: BatfsKO1 [JWA17]


title: Reg1sKO4 [JWA16]


title: Reg1sKO3 [JWA15]


title: Reg1sKO2 [JWA14]


title: Reg1sKO1 [JWA13]


title: WT4 [JWA12]


title: WT3 [JWA11]


title: WT2 [JWA10]


title: WT1 [JWA9]


title: m10

type: RNA

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

institute: Institute of Pharmacology

description: SAMPLE 24

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization using GenomeStudio 2011.1

label: biotin

source_name: anterior cingulate cortex (ACC), sham_2wk

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit

extract_protocol: RNeasy Lipid Tissue Mini kit

treatment_protocol: Cuff, Sham

tag: gender

value: male

value: sham

tag: time

value: ACC


title: m5

description: SAMPLE 21


title: m18

description: SAMPLE 22


title: m16

description: SAMPLE 20


title: m14

description: SAMPLE 18

source_name: anterior cingulate cortex (ACC), cuff_2wk

value: cuff


title: Dpt KO CCL4 #9

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

description: Transcriptomic liver Dpt KO CCL12

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: Affymetrix GeneChip Command Console software (AGCC).  RMA used as normalization method.

source_name: C57Bl6J adult female mouse

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: 10- to 12-week-old female Dpt-null mice and their WT littermates were used.

extract_protocol: RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: s.c. injection were performed 3 times a week with 0.1 ml/kg of a 2% CCl4 solution for 1 week, then 4% (week 2), 5% (week 3), 6% (week 4), and 8% (week 5-8). Livers were harvested 24 hours after the last injection

value: liver

tag: background strain

value: KO for Dpt

tag: Sex

value: female

tag: age

value: 10-12 weeks


title: JWR126_TIL_KO4

data_processing:
The raw reads were trimmed for adapter sequences using Trimmomatic v.0.36 using parameters ILLUMINACLIP:adapter.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:18 MINLEN:32
followed by mapping to mm9 reference genome downloaded from gencode release M1 (https://www.gencodegenes.org/mouse/releases.html) using star v.2.5.2b. with default parameters
Reads were summarized at genelevel using python script htseq-count. Differential expression analysis was performed using R package DEseq2 v. 1.18.1.
Genome_build: mm9
Supplementary_files_format_and_content: gene level counts for each samples using Htseq-counts in txt format

growth_protocol: CD8+ T cells were sorted from sgRNA transduced OT-I cells from the B16-Ova melanoma tumor and peripheral lymph nodes

extract_protocol:
For bulk RNA-seq, RNA was quantified using the Quant-iT RiboGreen assay (Life Technologies)
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020595)

tag: cell subtype

value: CD8+ T cells from tumors


title: m15

description: SAMPLE 14


title: m3

description: SAMPLE 13


title: m7

description: SAMPLE 23


title: m17

description: SAMPLE 16


title: JWR126_TIL_KO5


title: m2

description: SAMPLE 19


title: Dpt KO CCL4 #7

description: Transcriptomic liver Dpt KO CCL10


title: m36

description: SAMPLE 12

source_name: anterior cingulate cortex (ACC), sham_8wk


title: Dpt KO CCL4 #8

description: Transcriptomic liver Dpt KO CCL11


title: m4

description: SAMPLE 15


title: JWR126_TIL_KO2


title: Dpt KO CCL4 #2

description: Transcriptomic liver Dpt KO CCL5


title: Dpt KO CCL4 #6

description: Transcriptomic liver Dpt KO CCL9


title: WT CCL4 #8

description: Transcriptomic liver WT CCL11

value: WT


title: Dpt KO CCL4 #4

description: Transcriptomic liver Dpt KO CCL7


title: m9

description: SAMPLE 17


title: Dpt KO CCL4 #5

description: Transcriptomic liver Dpt KO CCL8


title: Dpt KO CCL4 #3

description: Transcriptomic liver Dpt KO CCL6


title: Dpt KO CCL4 #1

description: Transcriptomic liver Dpt KO CCL4


title: WT CCL4 #9

description: Transcriptomic liver WT CCL12


title: m28

description: SAMPLE 11


title: JWR126_TIL_KO1


title: m35

description: SAMPLE 10


title: m27

description: SAMPLE 9


title: WT CCL4 #6

description: Transcriptomic liver WT CCL9


title: JWR122_TIL_WT3

value: wildtype


title: WT CCL4 #7

description: Transcriptomic liver WT CCL10


title: JWR126_TIL_KO3


title: CiPC-d1-3 [ATAC-Seq]

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (42 nt reads, paired end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1e-7, without control file, and with the -nomodel option.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: Reprogrammed cells (CiPC) at d11

growth_protocol: MEFs were routinely maintained in IMR90 medium and photoreceptor induction medium was used to concert MEFs to photoreceptor like cells.

extract_protocol:
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were thawed in a 37oC water bath, pelleted, washed with cold PBS. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter)

treatment_protocol: Treatments of MEFs by sequencial addition of five chemicals in induction medicum to derive photoreceptor like cells

value: MEF derived photoreceptor like cells

value: Strain (Nrl-GFP)


title: m25

description: SAMPLE 8


title: WT CCL4 #5

description: Transcriptomic liver WT CCL8


title: JWR122_TIL_WT2

value: sgRNA transduced OT-I cells


title: CiPC-d1-1 [ATAC-Seq]


title: CiPC-d1-2 [ATAC-Seq]


title: JWR117_PLN_KO5

value: CD8+ T cells from peripheral lymph nodes


title: JWR122_TIL_WT1


title: JWR117_PLN_KO4


title: RI-d8-3 [ATAC-Seq]

source_name: Reprogramming intermediate at d8

value: MEF derived photoreceptor intermediates


title: m21

description: SAMPLE 7


title: RI-d8-2 [ATAC-Seq]


title: m42

description: SAMPLE 6

source_name: anterior cingulate cortex (ACC), cuff_8wk


title: JWR117_PLN_KO3


title: RI-d8-1 [ATAC-Seq]


title: WT CCL4 #4

description: Transcriptomic liver WT CCL7


title: m38

description: SAMPLE 5


title: m29

description: SAMPLE 2


title: JWR117_PLN_KO2


title: m39

description: SAMPLE 4


title: RNAseq_Ring1_KO_Rnf2_flfl_FGO_rep3

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

data_processing: RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11 for each replicate. Transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.

growth_protocol: Ring1−/−; Rnf2f/f mice with or without Zp3-cre were maintained as described in Posfai et al. 2012 (PMID:22499591)

extract_protocol:
For RNA isolation, 15 GV oocytes from one mouse were pooled and RNA was extracted using the RNAEasy Micro Kit (Qiagen,74004) according to the manufacturer’s instructions. Total RNA was quantified and checked for quality on Agilent’s BioAnalyzer using the RNA 6000 Pico Kit (Agilent, 5067-1513).
RNA was amplified and converted to cDNA using the Ovation v2 Kit (NuGen, 7102). Sequencing libraries were prepared with the Truseq DNA LT kit (Illumina, FC-121-2001) and multiplexed, barcoded libraries were sequenced on an Illumina HiSeq instrument.

treatment_protocol: Cumulus oocyte complexes were isolated from ovaries of approx. 3 months old females. Granulosa cells were removed by repeated pipeting using a fine-pulled capilary glass needle in M2 medium. Oocytes were washed twice in M2 medium and subsequently washed twice in DNA suspension Buffer (TEKnova, PNT0221).

value: mixed FVB, 129/Sv and C57BL/6J

value: Ring1 -/-; Rnf2 f/f

tag: tissue/cell type

value: germinal vesicle (GV) stage mouse oocytes


title: m33

description: SAMPLE 3

value: male

value: ACC


title: MEF-3 [ATAC-Seq]

source_name: Mouse embryonic fibroblasts at passage 2

value: Fibroblast like cells


title: WT CCL4 #3

description: Transcriptomic liver WT CCL6

value: liver


title: WT CCL4 #1

description: Transcriptomic liver WT CCL4

value: female


title: RNAseq_Ring1_KO_Rnf2_flfl_FGO_rep2


title: MEF-2 [ATAC-Seq]


title: JWR117_PLN_KO1


title: Dpt KO control #7

description: Transcriptomic liver Dpt KO control

value: KO for Dpt

value: Olive oil

value: 10-12 weeks


title: Dpt KO control #8

description: Transcriptomic liver Dpt KO control


title: WT CCL4 #2

description: Transcriptomic liver WT CCL5

value: WT


title: Dpt KO control #10

description: Transcriptomic liver Dpt KO control


title: JWR122_TIL_WT4

value: CD8+ T cells from tumors

value: wildtype


title: JWR113_PLN_WT4

value: sgRNA transduced OT-I cells


title: RNAseq_Ring1_KO_Rnf2_flfl_FGO_rep1


title: MEF-1 [ATAC-Seq]

value: Strain (Nrl-GFP)


title: RNAseq_Ring1_Rnf2_dKO_FGO_rep3

value: Ring1 -/-; Rnf2 f/f; Zp3-cre


title: PP2 (scRNA-Seq)

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
The sequencing libraries were sequenced using Nextseq 500 platform.
Each of the samples was analyzed by cellranger (version 1.2.1) mkfastq , outputs were used as input for cellranger (version 2.0.0) count, run with the option --force-cells=1500  and using the 10X prebuilt  mm10 reference database version 1.2.0.    Sequencing reads were first aligned to mm10 reference using STAR V2.5.1b (Dobin et al., 2013) and then aligned to annotated transcripts, which were part of the Cell Ranger version 2.1 pipeline (https://www.10xgenomics.com). A customized pre-mRNA reference package was generated to capture all the intronic reads in addition to reads that are mapped to exons.
The outputs from CellRanger were further analyzed using the Seurat package V2.3 (Butler et al., Nature Biotechnology 2018) and R 3.5.
Using Seurat we performed  gene filtering  (gene must appear in 3 cells of a sample)  and merging of the cells of both samples to one set.  Cell  filtering was  based on the number of genes per cell (must be between 400 and 5000) ,on the number of UMI counts per cell (between 1000 and 10,000), and the percent of mitochondria genes lower than 0.25 percent.
Clusters were created with 900 variable genes and 11 PCs. The cluster names were replaced with the cell type identity based on the differentially expressed genes (marker genes).
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing the gene average log normalized expression per cluster

source_name: Neurohypophysis

extract_protocol:
Neurohypophyses were dissected and pooled in ice cold HBS -/- buffer. Single cell suspension were achieved by Liberase TM and Papain digestion. Single cell library preparation was conducted using 10X Genomics Chromium Single Cell Kit Version 2
The libraries were sequenced using an Illumina NextSeq 500 High Output v2 kit (R1 26 cycles, R2 58 cycles) following the manufacturer’s instructions.

value: Neurohypophysis

value: 3 months


title: JWR113_PLN_WT2

value: CD8+ T cells from peripheral lymph nodes


title: RNAseq_Ring1_Rnf2_dKO_FGO_rep2

value: mixed FVB, 129/Sv and C57BL/6J

value: germinal vesicle (GV) stage mouse oocytes


title: Dpt KO control #9

description: Transcriptomic liver Dpt KO control


title: Dpt KO control #5

description: Transcriptomic liver Dpt KO control


title: JWR113_PLN_WT1


title: JWR113_PLN_WT3


title: m22

description: SAMPLE 1

value: male

value: cuff

value: ACC


title: Dpt KO control #6

description: Transcriptomic liver Dpt KO control

value: liver

value: KO for Dpt

value: female


title: RNAseq_Ring1_Rnf2_dKO_FGO_rep1


title: PP1 (scRNA-Seq)


title: ATAC-SJMMNORM060335_G1-JWA8-KO4

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm9 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM37_um.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm9
Supplementary_files_format_and_content: average bigwig files by using the centre 80 bp of fragments and scaling them to 30 M nucleosome-free reads

growth_protocol: CD8+ T cells were sorted from sgRNA transduced OT-I cells from the B16-Ova melanoma tumor


title: Susceptible Receptor Null

city: Charlottesville

first: Awndre

middle: E

last: Gamache

state: VA

address: 1122 Forest Hills Ave., B

department: Bierne B. Carter Center for Immunology Research

institute: University of Virginia

data_processing:
Cell Ranger
Genome_build: mm9

source_name: Natural Killer cells

extract_protocol:
3x Negative enrichement - Miltenyi MACs NK cell isolation kit used per manufacturers instructions
Single cell cDNA libraries were separately prepared from negatively enriched NKCL-Dk, NKCL, and NKCGO1-Dk spleen NK cells (>80% viability, 90-98% purity) by the UVA Genome Analysis and Technology Core (GATC) using a Chromium Controller instrument (10X Genomics) and the Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics) following the manufacturer’s protocol.  The indexed libraries were sized using the Agilent 4200 TapeStation and pooled into equimolar concentration.

treatment_protocol: Mice were infected with 5x104 PFU MCMV four days prior to sacrifice.

value: Natural Killer Cells

tag: isolation

value: 3x Negative enrichement - Miltenyi MACs NK cells kit


title: Susceptible Ligand Null


title: s14_TSS-Seq_hen2_RT_rep1

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina Casava v1.7 software was used for basecalling.
PlaNET-Seq: 1) Trim 4bp UMI barcodes from 5' ends of both R1 and R2 reads (UMI-Tools extract v0.5.3); 2) Align R2 reads to TAIR10 (STAR v2.5.2b; --outSAMmultNmax 1 --alignEndsType Extend5pOfRead1 --clip3pAdapterSeq GATCGTCGGACT); 3) Sort BAM files (Samtools v1.3.1); 4) Remove PCR duplicates (UMI-Tools dedup); 5) Remove reads aligned to rRNA, tRNA, snRNA or snoRNA loci from Araport11 (BEDTools v2.17.0); 6) Remove reads with MAPQ < 10 (Samtools v1.3.1); 7) Import BAM files into R environment v3.5.1 (GenomicAlignments_1.18.1, GenomicRanges_1.34.0); 8) Flip the strand orientation; 9) Skip all split reads; 10) Skip reads with 3' end overlapping known splice sites (combined from TxDb.Athaliana.BioMart.plantsmart28_3.2.2 and Araport11); 11) Convert reads to genomic coverage (separately for + and - strands); 12) Export as BigWig files (rtracklayer_1.42.2). TSS-Seq: data processing was described previously in Nielsen et al., 2019 (PMID 30707695).
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files show strand-specific sequencing coverage with single base resolution (no signal smoothing, transformation or normalization were applied). For TSS-Seq, only positions with coverage above 2 tags were reported.

organism: Arabidopsis thaliana

source_name: TSS-Seq of hen2-2 mutant grown at 22⁰C

growth_protocol: PlaNET-Seq: Arabidopsis seedlings were grown on plates (1/2 Murashige and Skoog medium, 1% sucrose) with a 16h light/8h dark cycle at 22°C/18°C. Light intensity during day hours was approximately 100 µE m-2 s-1. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695).

extract_protocol:
PlaNET-Seq: Nuclei were isolated from 3 grams of seedlings. Chromatin was solubilized by DNase I treatment. Nascent RNA fraction was enriched by immunoprecipitation of FLAG-tagged RNAPII elongation complexes using anti-FLAG antibody (F3165, Sigma-Aldrich) coupled to Dynabeads Protein G. Finally, RNAPII complexes were eluted from Dynabeads by 3xFLAG peptide, and the nascent RNA was purified using miRNeasy kit (QIAgen). TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695).
PlaNET-Seq: NGS libraries were constructed from nascent RNA using Small RNA-Seq Kit v3 (Bioo Scientific). The original protocol was modified to incorporate alkaline RNA fragmentation step after 3' adapter ligation. TSS-Seq: as described previously in Nielsen et al., 2019 (PMID 30707695).

treatment_protocol: For inhibition of splicing, seedlings were grown on filter paper covered 1/2 MS + 1% sucrose for 10 days then transferred to either DMSO or 5 µM pladienolide B (Santa Cruz) containing plates for 6 hours. For cold treatment, 10-day old seedlings grown were transferred to 4°C and approximately 25 µE m-2 s-1 for either 3 hours or 12 hours.

tag: ecotype background

value: Columbia (Col-0)

value: 14 day

value: Whole seedlings

value: grown at 22⁰C

tag: protocol

value: TSS-Seq


title: ATAC-SJMMNORM060335_G1-JWA6-KO2

tag: cell type

value: sgRNA transduced OT-I cells

value: CD8+ T cells from tumors

tag: strain


title: s15_TSS-Seq_hen2_RT_rep2

tag: tissue


title: Dpt KO control #3

description: Transcriptomic liver Dpt KO control

tag: genotype

value: Olive oil

value: 10-12 weeks


title: ATAC-SJMMNORM060335_G1-JWA7-KO3


title: Resistant Wt


title: Dpt KO control #4

description: Transcriptomic liver Dpt KO control

tag: treatment


title: ATAC-SJMMNORM060335_G1-JWA5-KO1


title: CD45RBLO_Mem_4

city: Atlanta

first: Mandy

middle: L

last: Ford

state: GA

address: 101 Woodruff Circle, WMB 5105

department: Surgery

institute: Emory University

description:
CD45RBlo_4
processed data file: 20171116_CD45RB_RNASeq_Counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using samtools, counted using featurecount,
Differential expression analysis was performed using DeSeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 20171116_CD45RB_RNASeq_Counts.txt: Tab-delimited text file includes normalized counts for each sample.

source_name: Spleen

growth_protocol: Mice were infected with 2x10^5 pfu LCMV Armstrong i.p., on week 6 post-infection (day 42-45), splenocytes were stained with antibodies and Kb NP396 tetramer and flow sorted to >99% purity.

extract_protocol:
RNA was extracted using the Qiagen Allprep DNA/RNA Micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: CD45RBlo NP396+ CD8+ memory T cells

tag: time point

value: Post-LCMV Armstrong 42-45 days


title: CD45RBLO_Mem_3

description:
CD45RBlo_3
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: Healthy control Tfhs 8

city: Berkeley

first: Chenling

last: Xu

state: CA

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

data_processing:
RNA-seq reads were aligned to the RefSeq hg38 transcriptome (GRCh38.2) using Bowtie2.
Data processed with Expectation Maximization (RSEM) toolkit to estimate expected counts over RefSeq transcripts.
enforcing (> 107k reads, >10% read alignment (forced), >93.3% common genes detected; corresponding to zcut = 20)
Genome_build: GRCh38.2

organism: Homo sapiens

source_name: CSF Tfhs

extract_protocol:
CSF was taken by lumbar puncture. Cells were stained with Antibodies against CD3, CD4, CXCR5 and Tfhs (CD3+CD4+CXCR5+ cells) were flow sorted. RNA was isolated and samples were prepared using a modified version of the SmartSeq2 protocol. Briefly, unquantified purified RNA was used as input. Reaction volumes were scaled up and the number of PCR cycles during cDNA amplification adjusted accounting for the higher number of input cells compared to the original protocol.
Library Preparation was done by the Next Ultra II FS DNA Library Prep Kit (New England Biolabs) using 1-3 ng of cDNA as input.

value: CSF Tfh cells


title: Healthy control Tfhs 9


title: CD45RBLO_Mem_2

description:
CD45RBlo_2
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: Dpt KO control #2

description: Transcriptomic liver Dpt KO control

value: liver


title: Healthy control Tfhs 7


title: ATAC-SJMMNORM060331_G1-JWA4-WT4

tag: genotype/variation

value: wildtype


title: ATAC-SJMMNORM060331_G1-JWA3-WT3


title: CD45RBLO_Mem_1

description:
CD45RBlo_1
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: Healthy control Tfhs 6


title: ATAC-SJMMNORM060331_G1-JWA2-WT2


title: Healthy control Tfhs 5


title: Dpt KO control #1

description: Transcriptomic liver Dpt KO control

value: KO for Dpt

value: female


title: WT control #6

description: Transcriptomic liver WT control

value: WT


title: CD45RBHI_Mem_3

description:
CD45RBhi_3
processed data file: 20171116_CD45RB_RNASeq_Counts.txt

value: CD45RBhi NP396+ CD8+ memory T cells


title: WT control #5

description: Transcriptomic liver WT control


title: WT control #8

description: Transcriptomic liver WT control


title: CD45RBHI_Mem_4

description:
CD45RBhi_4
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: Healthy control Tfhs 4


title: WT control #4

description: Transcriptomic liver WT control


title: ATAC-SJMMNORM060331_G1-JWA1-WT1


title: CD45RBHI_Mem_2

description:
CD45RBhi_2
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: Healthy control Tfhs 3


title: CD45RBHI_Mem_1

description:
CD45RBhi_1
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: WT control #7

description: Transcriptomic liver WT control


title: Sample 15

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

description: Group 2 are mice that have a single X chromosome of a paternal origin,  and a Y chromosome that lacks the male Y-specific region Sry making them effectively female.

data_processing:
Overall sequece quality of each samples was assessed using FASTQC (version 0.11.3) and to identify specific reads and regions that may benefit from trimming.
Sequence trimming was done using TrimGalore (version 0.4.0) was employed to trim low-quality bases (quality score lower than 20), adapter sequences (stringency 6) and end-repair bases from the 3’ end of reads.
Alignment and methylation calling of trimmed sequences was done using Bismark 56 (version 0.14.3).
Reads were aligned to the UCSC mm10 reference genome (iGenomes) using Bowtie2 57 (version 2.2.1) with default parameters settings, except for maximum number of mismatches in seed alignment (N) set to 1, and length of seed substrings (L) set to 20. Methylation calls were reported for all nucleotides with a read depth of at least 10. Sites with >500 read depth were removed due to the likelihood that they are biased by duplicates from PCR amplification.
Overall quality of methylation calls and coverage was determined using methylSig 58 R package (0.4.4) as well as pairwise differential methylation. For each pairwise comparison methylSig uses a beta-binomial approach to calculate differential methylation statistics, accounting for variation among replicates within each group. We adjusted the p-values for multiple testing using the FDR approach, and considered sites to be differentially methylated when they had a percent change in methylation of at least 15% and a qvalue smaller than 0.1.
Sites and regions were annotated using UCSC Genome Browser’s annotations for CpG islands, promoters and other genetic regions.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file for each sample containing chromosome location and percent methylation of each methylation site

source_name: CD4+ T cells

extract_protocol:
Genomic DNA from CD4+ T cells of XmY*x and XpY*x mice were isolated using AllPrep DNA/RNA Mini Kit (Qiagen).
25ng of genomic DNA was digested with MspI, a restriction enzyme preferentially cutting at CpG rich sites. This digested DNA was purified using phenol:chloroform extraction and ethanol precipitation, before blunt-ending and phosphorylation.  A single A nucleotide was added to the 3’end of the fragments in preparation for ligation of methylated and single indexed adapter duplex with a T overhang. The ligated fragments were then cleaned, and processed for size selection on agarose gel. Selected fragments were treated with bisulfite, followed by PCR amplification to convert unmethylated cytosines to thymine nucleotide. After cleanup with AMPure XP beads, libraries were quantified using the Qubit assay and TapeStation High Sensitivity D1000 kit. . Single-end reads of 50 base pairs were obtained for each library by sequencing 3 samples per lane using HiSeq4000 (Illumina).

value: SJL

value: XpY*X

tag: litter

value: Group 2


title: Sample 17

tag: background strain


title: Sample 14


title: WT control #2

description: Transcriptomic liver WT control

tag: Sex


title: Healthy control Tfhs 1


title: Healthy control Tfhs 2


title: WT control #3

description: Transcriptomic liver WT control

tag: age


title: CD44lo_CD8_2

description:
2_naive
processed data file: 20171116_CD45RB_RNASeq_Counts.txt

value: Naive CD8+ T cells

value: Naive 6-8 weeks


title: CD44lo_CD8_3

description:
3_naive
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: Sample 13


title: CD44lo_CD8_1

description:
1_naive
processed data file: 20171116_CD45RB_RNASeq_Counts.txt


title: NCC-RbC-51 + BMSC direct coculture control - 3

city: Chennai

first: Krishnakumar

last: Subramanian

address: Sankara Nethralaya, College road, Nungambakkam

department: Department of Ocular Pathology

country: India

institute: Vision Research Foundation

hyb_protocol: Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on Primeview Human Gene Expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymmetrix Genechip scanner.

data_processing: The data was analyzed using RMA algorithm with quantile normalization.

label: Biotin

source_name: Pooled control of RB cells (NCC-RbC-51) and BMSC

label_protocol: Biotinylated cRNA was prepared from 100 ng total RNA according to standard Affymmetrix protocol.

growth_protocol: RB cells and BMSC cells were seeded together in 6 well plates and allowed to grow for 24 h under serum starved condition.

extract_protocol: Total RNA was isolated with Qiagen Rneasy kit following manufacturer's protocol

value: RB cells (NCC-RbC-51)


title: Sample 6

description: Group 1 are mice that have a single X chromosome from a maternal origin,  and a Y chromosome that lacks the male Y-specific region Sry making them effectively female.

value: XmY*X

value: Group 1


title: WT control #1

description: Transcriptomic liver WT control

value: Olive oil

value: 10-12 weeks


title: MS patient Tfhs 9

value: CSF Tfh cells


title: NCC-RbC-51 + BMSC direct coculture control - 2


title: NCC-RbC-51 + BMSC direct coculture test - 3

source_name: RB cells (NCC-RbC-51) after 24 h coculture with BMSC


title: Sample 5


title: MS patient Tfhs 8


title: MS patient Tfhs 7


title: NCC-RbC-51 + BMSC direct coculture control - 1


title: MS patient Tfhs 6


title: NK-V-3

first: Stephen

middle: R

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: NK-RPKM.xlsx

data_processing:
BCL conversion and Multiplexing (Casava 1.8.2)
Map to mm10 (Tophat 2.1.1)
Calculate RPKM (Partek GS 7.18.0723)
Calculate ANOVA (Partek GS 7.18.0723)
Genome_build: mm10
Supplementary_files_format_and_content: RPKM and ANOVA results in Excel format

source_name: splenic NKp46+ CD3- sorted cells

growth_protocol: cells were stored in Trizol LS immediately after sorting

extract_protocol:
trizol LS
NEBNext Ultra II RNA Library Prep

treatment_protocol: animal were treated or not for oral gavage for 1 week with tofacitinib

value: BALB/C

tag: organ

value: spleen

value: Vehicle


title: NK-T-2

description: NK-RPKM.xlsx

value: Tofacitinib


title: NK-T-1

description: NK-RPKM.xlsx


title: MS patient Tfhs 5


title: NK-V-2

description: NK-RPKM.xlsx


title: Sample 1


title: Sample 4


title: MS patient Tfhs 4


title: NK-V-1

description: NK-RPKM.xlsx


title: 30dox50polys3

city: Amsterdam

first: Georges

last: Janssens

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were subjected to quality control FastQC (Andrews, 2010) trimmed using Trimmomatic v0.32 (Bolger et al., 2014) and aligned to either the C. elegans (worm) or M. musculus (mouse) genomes obtained from Ensembl, wbcel235.v91 and GRCm38v87, respectively, using HISAT2 v2.0.4 (Kim et al., 2015).
Counts were obtained using HTSeq (v0.6.1, default parameters) (Anders et al., 2015) using the corresponding GTF taking into account the directions of the reads.
Statistical analyses were performed using the edgeR (Robinson et al., 2010) and limma/voom (Ritchie et al., 2015) R packages.
All genes with no counts in any of the samples were removed whilst genes with more than 2 count-per-million reads (CPM) in at least 4 of the samples were kept.
Count data were transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method (Robinson et al., 2010) and precision weighted using voom (Law et al., 2014), available as a supplementary table with the publication.
Genome_build: wbcel235.v91 (worm) or GRCm38v87 (mouse)
Supplementary_files_format_and_content: csv file of CMPs (counts per million) for RNAseq data mapped to gene level for each sample

source_name: Whole liver

growth_protocol: Worms: worms were cultured at 20°C on nematode growth medium (NGM) agar plates seeded with OP50 strain Escherichia coli as described before (Molenaars et al., 2018). Synchronized worms were harvested and snap frozen at L4 larval stage for mRNA isolation. Mice: C57BL/6J germ-free mice were used.

extract_protocol:
For isolation of total mRNA, whole worms or liver tissue were homogenized with a 5 mm steel bead using a TissueLyser II (Qiagen) for 5 min at frequency of 30 times/sec in the presence of TRIzol (Invitrogen), then the isolation was continued according to manufacturer’s protocol. Polysomal fractions from two experiments were pooled and mRNA was extracted using TRIzol LS (Invitrogen) according to the manufacturer’s protocol. Contaminating genomic DNA was removed using RNase-Free DNase (Qiagen) and samples were cleaned up with the RNeasy MinElute Cleanup Kit (Qiagen).
The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420). Briefly, rRNA was depleted from total RNA using the RiboZero kit. After fragmentation of the rRNA reduced RNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product.

treatment_protocol: Worms: For RNAi knock down experiments, 5000 synchronized eggs were plated on NGMi (containing 2 mM IPTG) with a bacterial lawn of either E. coli HT115 (RNAi control strain, containing an empty vector) or mrps-5 RNAi bacteria. Mice: C57BL/6J germ-free mice were treated for two weeks with either amoxicillin (50 mg/kg/d), doxycycline (50 mg/kg/d), or a high dose doxycycline (500 mg/kg/d) in the drinking water supplemented with sucrose. Mice were sacrificed after 16 hours of fasting, and the livers were harvested and snap frozen in liquid N2.

value: Liver

value: doxycycline

tag: molecule subtype

value: polysomal RNA


title: Weri-Rb1 + BMSC direct coculture control - 3

source_name: Pooled control of RB cells (Weri-Rb-1) and BMSC

value: RB cells (Weri-Rb-1)


title: NCC-RbC-51 + BMSC direct coculture test - 2


title: ILC-T-2

description: ILC-RPKM.xlsx

source_name: Liver CD3- Nkp46+ DX5dim TRAIL+ sorted ILC

value: liver


title: NCC-RbC-51 + BMSC direct coculture test - 1


title: MS patient Tfhs 2


title: 29dox50polys2


title: MS patient Tfhs 3


title: ILC-T-1

description: ILC-RPKM.xlsx


title: Sample 3

value: SJL


title: Crist_muc_stb_day6

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
Sequencing reads were aligned to Cmucedo_v1 genome assembly using splice-aware aligner Hisat2 v2.1.0.
Reads were assigned to genomic features using featureCounts v1.5.1 using "-O -M --fraction -p -t exon -g gene_id -a Cmucedo_v1_utr_mt_prod.gtf" options for paired-end, and " -O -M --fraction -t exon -g gene_id -a Cmucedo_v1_utr_mt_prod.gtf" for signle-end reads.
Genome_build: Cristatella mucedo genome Cmucedo_v1
Supplementary_files_format_and_content: Raw read count values in tab-separated text columns

molecule: polyA RNA

organism: Cristatella mucedo

source_name: C. mucedo statoblasts

growth_protocol: Adult colonies were collected from freshwater stream and kept in aquarium at room temperature. Statoblasts were stored in the freezer at -80°C, and allowed to differentiate in an aquarium at room temperature.

extract_protocol:
Two different types of morphological dissection were performed. In the first case, the colony was divided into central and peripheral (edge) zones. In the second case, elongated colonies were divided into middle and terminal parts. In case of statoblast differentiation, thawed statoblasts were allowed to grow in aquarium for the specified number of days, after which the whole colony was sequenced. The RNA was extracted using Zymo Research Quick RNA mini extraction kit (R1050, Zymo Research, Irvine, California, USA). For every sample, two biological replicates were made.
Poly-A RNA fraction was enriched using oligo-dT magnetic beads. The libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7760, New England BioLabs, Ipswich, Massachusetts, USA). Paired-end sequencing was carried out using Illumina HiSeq 2500, and single-end sequencing was done on Illumina NextSeq 500.

value: isolate SBPEP1

value: wildtype

tag: developmental stage

value: day 6 after the beginning of differentiation


title: 28dox50polys1


title: ILC-V-3

description: ILC-RPKM.xlsx


title: ILC-V-2

description: ILC-RPKM.xlsx


title: Crist_muc_stb_day4

value: day 4 after the beginning of differentiation


title: Hi-C MCF7 6months Replicate 2

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.7.7 (Servant et al., 2015). The paired end reads were aligned separately using bowtie2 against the hg38 human build. Contact matrices were constructed at multiple resolutions and normalized suing ICE normalization algorithm (Imakaev et al. 2012).
Juicebox hic files were prepared using hicpro2juicebox script (Servant et al., 2015).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: allValidPairs files contain all valid interactions identified at multiple resolutions (10kb, 20kb, 40kb, 150kb, 500kb and 1Mb) using HiC-Pro pipeline. The validPairs are stored using a tab-delimited text format as described in (Servant et al., 2015). hic files contain compressed contact matrices at all resolutions. hic format can also be used to visualise Hi-C data in Juicebox (Durand et al., 2016; Robinson et al., 2018) or WashU Epigenome Browser (Zhou et al., 2013).

growth_protocol: MCF7 breast cancer cells were kindly given to our laboratory by Dr Liz Caldon (Garvan Institute, Australia). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS).  All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol:
Cells were cross-linked with formaldehyde, lysed and the intact nuclei was permeabilized. DNA was then cut with NcolI restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads.
Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing using the NEBNext DNA Master Mixes kit and the ligation of universal adapter was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: cell line

value: breast cancer

tag: resistant phynotype

value: responsive


title: Hi-C MCF7 6months Replicate 1


title: 26dox50s2

value: total RNA


title: Weri-Rb1 + BMSC direct coculture control - 1

tag: cell type


title: ILC-V-1

description: ILC-RPKM.xlsx

tag: strain

value: BALB/C


title: Crist_muc_stb_day2

value: day 2 after the beginning of differentiation


title: Weri-Rb1 + BMSC direct coculture control - 2


title: Weri-Rb1 + BMSC direct coculture test - 3

source_name: RB cells (Weri-Rb-1) after 24 h coculture with BMSC


title: Weri-Rb1 + BMSC direct coculture test - 2


title: Weri-Rb1 + BMSC direct coculture test - 1


title: Crist_muc_freezer

value: defrosted (freezer)


title: Hi-C MCF7 mid Replicate 2

tag: tissue


title: 24amox50polys3

value: amoxicillin (control)


title: 18mrps5monos3

organism: Caenorhabditis elegans

source_name: Whole worm

value: Whole worm

value: mrps-5 RNAi

value: monosomal RNA


title: Crist_muc_mid3

source_name: mature C. mucedo colonies

tag: genotype

tag: morphological dissection

value: middle part


title: 17mrps5monos2

tag: treatment


title: Crist_muc_mid2


title: 23amox50polys2

value: Liver

value: polysomal RNA


title: 16mrps5monos1


title: 27dox50s3

value: doxycycline


title: Hi-C MCF7 T0 Replicate 2


title: MS patient Tfhs 1

value: CSF Tfh cells


title: 22amox50polys1


title: Hi-C MCF7 mid Replicate 1


title: 25dox50s1


title: Crist_muc_ends3

value: isolate SBPEP1

value: wildtype

value: end part


title: 15mrps5polys3


title: Hi-C MCF7 T0 Replicate 1

value: breast cancer

value: responsive


title: 21amox50s3

value: total RNA


title: Crist_muc_ends1


title: 20amox50s2


title: 19amox50s1


title: 14mrps5polys2


title: Crist_muc_edge3

value: edge zone


title: Testis_13

city: Stanford

first: Alina

last: Isakova

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

description: sRNA-seq rep2

data_processing:
Illumina BaseSpace software used for demultiplexing
Sequenced reads were trimmed for adaptor sequence, and mapped to mm10 whole genome using STAR v2.5.1 (Dobin et al., 2013) with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --alignIntronMax 1 --outMultimapperOrder Random --clip3pAdapterSeq TGGAATTCTC --clip3pAdapterMMp 0.1
Transcript counts were calculated using a FeatureCounts, featureCounts -a Mus_musculus.GRCm38.90.gtf -M –primary -s 1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts Sample

source_name: Testis

extract_protocol:
Upon collection, tissue samples were submerged and preserved at -80C in RNAlater stabilization solution (ThermoFisher cat # AM7021) until further processing. Total RNA was isolated from ~ 100 mg of tissue using Qiagen miRNeasy mini kit (cat # 217004) and the Qiagen tissue lyser using 5 mm stainless steel beads. RNA integrity was assesses using Agilent Bioanalyzer using RNA 6000 pico kit (Agilent Technologies cat # 5067-1513).
Short RNA libraries were prepared following the Illumina TruSeq Small RNA Library Preparation kit (cat # RS-200-0012, RS-200-0024, RS-200-0036, RS-200-0048) according to the manufacturer’s protocol and size-selected using Pippin Prep 3% Agarose Gel Cassette (Safe Science) in a range 135 bp – 210 bp. Samples were pooled in batches of 48 and sequenced using the Illumina NextSeq550 instrument in a single-read, 50 or 75 -base mode.

tag: source type

value: Testis

value: Male


title: Crist_muc_cent2

value: central  zone


title: 13mrps5polys1

value: Whole worm

value: mrps-5 RNAi


title: Crist_muc_edge2


title: Scramble siRNA-2 [308_11_001]

city: JUPITER

first: Peiyuan

last: Zhang

state: FL

address: 110 Scripps Way

institute: TSRI

data_processing:
Illumina reads were trimmed and clipped for quality control in Trimmomatic v0.35.
Read quality was checked for each sample using FastQC v0.11.4.
Sequencing reads were mapped against the human reference genome (hg19, NCBI build 37) using Kallisto v0.42.4
Differential expression analysis was done using gene mode in Sleuth v0.30.0.
Genome_build: hg19, NCBI build 37
Supplementary_files_format_and_content: kallisto_table.csv: Comma-separated values file with Transcripts per million and scaled reads per base corresponding to each gene for each sample.

source_name: SH-SY5Y_Scramble siRNA

growth_protocol: Human neuroblastoma SH-SY5Y cells (ATCC, Manassas, VA, USA) were cultured in Dulbecco's Modified Eagle's Medium/F-12 1:1 mix medium (DMEM/F-12, GE Healthcare, Chicago, IL, USA) supplemented with 10% of fetal bovine serum (Atlanta Biologicals, Flowery Branch, GA, USA) and 1× Penicillin Streptomycin Solution (Corning). Cells in culture were maintained in a humidified incubator at 37°C in 5% CO2.

extract_protocol:
Cell culture media was removed and the monolayer was washed with DPBS.  Total RNA was extracted using a miRNeasy Mini Kit (Qiagen) using an on-column DNase I treatment, following the manufacturer's protocol.
A Qubit 2.0 Fluorometer (Invitrogen) and an Agilent Technologies 2100 Bioanalyzer with an RNA nano chip were used to quantify and assess the quality of RNA, respectively.  Only samples with RNA Integrity Number > 8.0 were used.  NEBNext rRNA depletion modules (Catalog #: E6310L, New England Biosciences) were used to deplete rRNA on 500 ng of total RNA, according to manufacturer’s instructions.  A NEBNext Ultra II Directional RNA kit (Catalog #: E7760, New England Biosciences) was used for library preparation according to the manufacturer’s instructions.  RNA samples were then chemically fragmented, primed with random hexamers, and reverse transcribed to convert fragmented RNA to first strand cDNA.  The RNA template was removed and dUTP was incorporated in place of dTTP, after which the second strand of cDNA was synthesized by end repair and 3’ end adenylation.  A hairpin loop adaptor was used to ligate an adaptor A corresponding T nucleotide on the hairpin loop adaptor was used to ligate an adaptor to the double-stranded cDNA.  Uracil-specific excision reagent (USER) enzyme was then used to remove the dUTP in the loop, as well as other incorporated U’s in the second strand.  Final libraries were generated by PCR amplifying adaptor ligated DNA with Illumina barcoding primers, where fragments with both 5’ and 3’ adaptors would be enriched in the final PCR step.  Libraries were normalized to 2 nM, validated by a Bioanalyzer DNA chip, pooled equally, and then sequenced on a Illumina NextSeq 500 v2.5 flow cell (1.8 pM) using paired-end chemistry (2 × 40 bp).  Approximately 20-25 million reads were generated per sample with a base quality score >Q30 (less than 1 error per 1000 bp).

treatment_protocol: For compound treatment (Synucleozid or DMSO Vehicle), compound stocks in DMSO were diluted in growth medium and added to cells for 48 h. For siRNA treatment, cells were transfected with 0.1 microM alpha-synuclein siRNA (ON-TARGETplus Human SNCA siRNA - SMARTpool) or scramble siRNA (ON-TARGETplus Non-targeting siRNA) using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions for 48 h.

value: human neuroblastoma cell line

value: 48 h of Scramble siRNA treatment


title: Scramble siRNA-1 [308_10_001]


title: 11mrps5s2


title: Testis_12

description: sRNA-seq rep2


title: alpha-synuclein siRNA-3 [308_09_001]

source_name: SH-SY5Y_alpha-synuclein siRNA

value: 48 h of alpha-synuclein siRNA treatment


title: Crist_muc_cent1


title: Testis_11

description: sRNA-seq rep2


title: Scramble siRNA-3 [308_12_001]


title: 09HT115monos3

value: empty vector

value: monosomal RNA


title: s13_WT_RT_mockIP

source_name: PlaNET-Seq of mock-IP

tag: ecotype background

value: Columbia (Col-0)

tag: genotype/variation

value: Wild type

value: 10 day

value: Whole seedlings

value: Nascent RNA

tag: protocol

value: PlaNET-Seq


title: alpha-synuclein siRNA-2 [308_08_001]


title: Synucleozid-2 [308_17_001]

value: 48 h of Synucleozid treatment


title: 08HT115monos2


title: 12mrps5s3

value: total RNA


title: 07HT115monos1


title: Synucleozid-3 [308_18_001]


title: 70.9 fL_RNAseq

city: Colleg Station

first: Michael

last: Polymenis

state: TX

address: 300 Olsen Blvd

department: Biochemistry and Biophysics

institute: Texas A&M University

description: Sample 21

data_processing:
The reads were aligned to the S. cerevisiae reference genome (version R64-1-1) using the Rsubread R language package.
First, an index was built using the command: buildindex(basename = “R64”, reference = “Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa”, gappedIndex=TRUE).
Then, for each of the 24 libraries, the paired end reads were aligned with the command: align(index = ‘R64’, readfile1 = ‘….fastq.gz’, readfile2 = ‘….fastq.gz’, type = “rna”).
To obtain the raw read counts (listed in the 'Matrix_non_normalized.xlsx' file), the output BAM files (from the align function described above) were then used in the featureCounts function of the Rsubread package, with the following command: featureCounts(files = “…subread.BAM”, ispairedEnd = TRUE, requireBothEndsMapped = TRUE, annotext = “Saccharomyces_cerevisiae.R64-1-1.95.gtf”, countChimericFragments = FALSE, isGTFAnnotationFile = TRUE).
To obtain the normalized values (listed in the 'Matrix_normalized.xlsx' file), we calculated the TPM (transcript per kilobase million) values as follows: First, we divided the read counts by the length of each gene in kilobases, to  obtain the reads per kilobase (RPK) values. Second, to obtain the “per million” scaling factor, we counted up all the RPK values in a sample and divided this number by 1,000,000. Third, we divided the RPK values by the “per million” scaling factor.
Genome_build: R64-1-1
Supplementary_files_format_and_content: raw counts and TPM values, listed for every gene and sample, in .xlsx files

organism: Saccharomyces cerevisiae

source_name: elutriated cell size pool

growth_protocol: The cells were cultivated in the standard, rich, undefined medium YPD (1% w/v yeast extract, 2% w/v peptone, 2% w/v dextrose), at 30 °C.

extract_protocol:
For each of the 24 samples, from ~3E+07 cells total RNA was prepared with the hot phenol method. Briefly, the frozen pellets were re-suspended in 0.4 ml TES buffer (10 mM Tris pH = 7.5, 10mM EDTA, 0.5% SDS), in DEPC-treated water, and ~0.05 ml glass beads were added. Then, 0.4 ml of acid phenol was added to each pellet, and the samples were incubated at 65 °C for 30 m, and vortexed briefly every 5 m during that time. The samples were centrifuged at 14,000 g for 5 m, and 0.3 ml of the top, aqueous layer were placed in a 2-ml screw-cap tube containing 1 ml cold ethanol with 40 μl of a 3M sodium acetate solution. The samples were incubated at 4 °C overnight and then centrifuged at 14,000 g for 20 m. The pellets were washed with 80% ethanol and centrifuged at 14,000 g for 5 m. The pellets were air-dried and resuspended in 25 μl of DEPC-treated water.
For the RNAseq libraries, we used the same approach we had described (Blank et al., 2017; EMBO J. 2017 Feb 15;36(4):487-502. doi: 10.15252/embj.201695050), except that we did not select for polyA-tailed RNAs. Instead, from total RNA, we depleted rRNA, using the ‘Ribo-Zero™ Magnetic Gold Kit (Yeast)’, according to the manufacturer’s instructions.
RNA-Seq, the 24 libraries were loaded onto 2 lanes (denoted L005 and L006 in the file names)

treatment_protocol: Briefly, elutriated wild type, G1 cells (diploid BY4743 background) were allowed to progress in the cell cycle until they reached the desired cell size. At that point, they were quenched (with 100 µg/ml cycloheximide and 0.1% sodium azide) and frozen away, and later pooled with cells of similar size.

tag: ploidy

value: diploid

tag: cell size


title: 74.3 fL_RNAseq

description: Sample 22


title: 06HT115polys3

value: polysomal RNA


title: DMSO Vehicle-3 [308_15_001]

source_name: SH-SY5Y_DMSO Vehicle

value: 48 h of DMSO treatment


title: 69.4 fL_RNAseq

description: Sample 20


title: 05HT115polys2

value: Whole worm


title: 10mrps5s1

value: mrps-5 RNAi


title: s10_WT_DMSO_rep2

source_name: PlaNET-Seq of wild type seedlings treated with DMSO

tag: age

value: DMSO


title: alpha-synuclein siRNA-1 [308_07_001]

value: human neuroblastoma cell line

value: 48 h of alpha-synuclein siRNA treatment


title: s09_WT_DMSO_rep1

tag: molecule subtype


title: DMSO Vehicle-2 [308_14_001]


title: 04HT115polys1

value: empty vector


title: 75.2 fL_RNAseq

description: Sample 23


title: s06_WT_Cold_12h_rep2

source_name: PlaNET-Seq of wild type exposed to 4⁰C for 12 hours

value: Columbia (Col-0)

value: 4⁰C for 12 hours


title: 03HT115s3


title: 65.7 fL_RNAseq

description: Sample 18


title: DMSO Vehicle-1 [308_13_001]


title: s12_WT_PlaB_rep2

source_name: PlaNET-Seq of wild type seedlings treated with DMSO + PlaB

value: Wild type

value: 10 day

value: DMSO + PlaB


title: 65.0 fL_RNAseq

description: Sample 17


title: 02HT115s2


title: s11_WT_PlaB_rep1

value: Whole seedlings

value: Nascent RNA

value: PlaNET-Seq


title: s05_WT_Cold_12h_rep1


title: Xlaevis_RGC_axons-2

city: Cambridge

first: Christine

last: Holt

address: Anatomy Bldg., Downing St.

department: Department of PDN

institute: University of Cambridge

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 was used for de-multiplexing and base-calling.
Sequence reads were mapped to the X. laevis v9.2 genome (Xenbase) using HISAT2 2.1.0 with default settings.
Transcript assembly and estimation of FPKM (Fragments Per Kilobase of transcript per Million fragments sequenced) values were performed using Cufflinks version 2.1.1.
Genome_build: X. laevis v9.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM for each gene

organism: Xenopus laevis

source_name: Retinal ganglion cell axons

growth_protocol: Eyes of stage 33/34-37/38 embryos of Xenopus laevis (Nieuwkoop and Faber, 1994) were cultuered on Boyden chamber device (1μm pore, Falcon Cell Culture Inserts, 10289270/ 353102, Thermo fisher scientific) coated on both sides of the membrane with poly-L-lysine (10μg/ml) and only on the bottom side with laminin (10μg/ml).

extract_protocol:
Total RNA was isolated from RGC axons separated from their cell bodies by a Boyden chamber device, using the Qiagen RNeasy Mini kit (Qiagen)
RNAs are reverse-transcribed, and then amplified by a PCR-based method (Tang et al., Nat Methods 6, 2009).

value: Retinal ganglion cells

tag: subcellular domain

value: axon


title: 64.5 fL_RNAseq

description: Sample 16

value: diploid


title: Xlaevis_RGC_axons-1


title: Synucleozid-1 [308_16_001]

tag: cell line

value: 48 h of Synucleozid treatment


title: s04_WT_Cold_3h_rep2

source_name: PlaNET-Seq of wild type exposed to 4⁰C for 3 hours

value: 4⁰C for 3 hours


title: FASR_WGS

data_processing:
Sequenced reads were aligned to human reference genome hg38 using bwa-mem v.0.7.9 and the GATK pipeline v.3.5 was used to identify duplicate reads, perform local re-alignment at indels, base quality score recalibration. Mapping statistics were calculated using QualiMap v.2.1.3.
Genome_build: hg38
Supplementary_files_format_and_content: vcf file containing copy number change data obtained using lumpy-sv v.0.2.4

source_name: FASR

growth_protocol: MCF7 breast cancer cells, and the corresponding endocrine resistant sub cell lines were kindly given to our laboratory by Dr Julia Gee (Cardiff University, UK). MCF7 cells were maintained in RPMI-1640 based medium containing 5% (v/v) fetal calf serum (FCS). Tamoxifen-resistant MCF7 (TAMR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and 4-OH-tamoxifen (1×10－7 M) (TAM). Fulvestrant-resistant MCF7 (FASR) cells were generated by the long-term culture of MCF7 cells in phenol-red-free RPMI medium containing 5% charcoal stripped FCS and fulvestrant (1×10－7 M) (FAS). Endocrine resistant sub lines were established and characterised following 6 months endocrine challenge. All cell lines were authenticated by short-tandem repeat (STR) profiling (Cell Bank, Australia) and cultured for less than 6 months after authentication.

extract_protocol:
DNA extracted from cell lines was used as a starting material for the Nextera TruSeq Library Preparation with PCR amplification. Each sample underwent paired-end (2 x 150bp) sequencing on Illumina HiSeq X Ten instrument generating around 35x coverage per sample.
Whole Genome Sequencing; Nextera TruSeq

value: breast cancer cells

tag: resistance phynotype

value: fulvestrant-resistant


title: s03_WT_Cold_3h_rep1


title: 01HT115s1

value: Whole worm

value: total RNA


title: 60.5 fL_RNAseq

description: Sample 15


title: L3W

first: Octavian

last: Voiculescu

address: Downing Street

department: Physiology, Development and Neuroscience

description: LCM embryo 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to galGal3 whole genome using bowtie 2-2.2.3
Genome_build: galGal3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gallus gallus

source_name: embryo

extract_protocol:
Qiagen miRNeasy Mini Kit columns (Cat.# 217004) were used to extract total RNA either from material dissected manually from live embryos or by laser-capture microdissection. Total amount of total RNA recovered was 1-7 ng.
Libraries were generated using SMARTer low RNA kit for Illumina Sequencing (Clontech)

value: stem zones elongating the axis

tag: cell population

value: ectoderm and mesoderm lateral to Organiser

tag: Stage

value: 9 somites


title: 67.5 fL_RNAseq

description: Sample 19

tag: strain


title: s02_WT_RT_rep2

source_name: PlaNET-Seq of wild type seedlings grown at 22/18⁰C

value: Columbia (Col-0)

value: Wild type

value: 10 day

tag: tissue

value: grown at 22/18⁰C


title: 60.8 fL_RNAseq

description: Sample 13


title: L3R

description: LCM embryo 3

value: mature Organiser


title: s01_WT_RT_rep1

value: Whole seedlings

value: Nascent RNA

value: PlaNET-Seq


title: TAMR_WGS reseq

source_name: TAMR

tag: cell type

value: tamoxifen-resistant


title: L2W

description: LCM embryo 2


title: TAMR_WGS


title: 59.7 fL_RNAseq

description: Sample 14

value: diploid


title: 75.9 fL_RNAseq

description: Sample 24


title: MCF7_WGS reseq

value: breast cancer cells

value: responsive


title: L1W

description: LCM embryo 1

value: 8 somites


title: MCF7_WGS


title: 53.9 fL_RNAseq

description: Sample 11


title: 56.4 fL_RNAseq

description: Sample 12


title: 55.9 fL_RNAseq

description: Sample 10


title: WGBS FASR

data_processing:
Sequencing reads from WGBS data were aligned to the human genome using version 1.2 of an internally developed pipeline Meth10X. It is publicly available and can be downloaded from https://github.com/luuloi/Meth10X (Nair et al., 2018). The pipeline backbone is built based on workflow control Bpipe (Sadedin SP at el. 2012) version 0.9.9.2 which mainly help to make automation, parallelism, restarting jobs and integration with cluster resource managers easier following the pipeline structure of P3BSseq (Luu PL, et al., 2017). Meth10X takes raw bisulphite reads in fastq files as inputs and produces a html report of all necessary metrics of bisulphite quality control and a tsv file of DNA methylation of 28 million CpG as rows and samples as columns. Briefly, adaptor sequences were removed using in-house bash script in paired end mode following prep kit guide. Bwa-meth verion 0.20 (https://github.com/brentp/bwa-meth) was then used to align reads to hg38 using bwa version 0.7.13 (https://github.com/lh3/bwa). The generated bam files are merged and marked duplication by Picard tools 2.3.0 (http://broadinstitute.github.io/picard). The merged bam files are checked with Qualimap 2.2.1 (Konstantin Okonechnikov at el. 2015) for quality as well as all metrics of WGBS. MethylDackel (https://github.com/dpryan79/MethylDackel) and Biscuit (https://github.com/zwdzwd/biscuit) are used to call DNA methylation and SNP. Samtools version 1.2 (Li H.et al. 2009) is used to manipulate bam files and all the plots are done with ggplot2 in R (H. Wickham. 2009).
Genome_build: hg38
Supplementary_files_format_and_content: BigWig file containing counts of methylated (C) and coverage (cov, methylated Cs + unmethylated Ts) at each CpG site assayed; Bed file containing DMRs identified using Bisulfighter (Saito et al., 2014).

extract_protocol: Library preparation and indexing were carried out as described in the CEGX TruMethyl WG user guide v2 wih minor improvements as described in Nair et al., 2018.

value: fulvestrant-resistant


title: 50.2 fL_RNAseq

description: Sample 9


title: L1R

description: LCM embryo 1

value: stem zones elongating the axis


title: WGBS TAMR


title: IDH MUT glioma cells treated with ATRA, Replicate 3

first: Nduka

last: Amankulor

address: 5117 Center Avenue

description: IDH MUT ATRA

hyb_protocol: Labeling, hybridization and scan were performed at the Healthcare Genomics Core at the University of Pittsburgh

data_processing: Data was processed using Partek Genomics Suite

source_name: IDH MUT primary glioma cells

growth_protocol: Primary glioma cells were grown in vitro in DMEM with 10% FBS. Cells were split when they reached 70% confluency

extract_protocol: After treatment, the cells were washed with PBS and RNA was extracted as per instructions from Qiagen RNAeasy kit

treatment_protocol: Treatment was started when cells were 50% confluent. The cells were treated with 1uM ATRA (final concentration) or DMSO for 48 hours

value: primary glioma cells

tag: genotype

value: IDH MUT

tag: treatment

value: ATRA


title: IDH MUT glioma cells treated with ATRA, Replicate 2

description: IDH MUT ATRA

scan_protocol: Labeling, hybridization and scan were performed at the Healthcare Genomics Core at the University of Pittsburgh


title: IDH MUT glioma cells treated with ATRA, Replicate 1

description: IDH MUT ATRA

label_protocol: Labeling, hybridization and scan were performed at the Healthcare Genomics Core at the University of Pittsburgh


title: 49.5 fL_RNAseq

description: Sample 8


title: WGBS MCF7


title: M3W

description: manual dissection embryo 3

value: ectoderm and mesoderm lateral to Organiser

value: 9 somites


title: 51.4 fL_RNAseq

description: Sample 7


title: M2W

description: manual dissection embryo 2


title: L2R

description: LCM embryo 2


title: 43.3 fL_RNAseq

description: Sample 6


title: M2R

description: manual dissection embryo 2


title: IDH MUT glioma cells treated with DMSO, Replicate 2

description: IDH MUT DMSO

value: DMSO


title: 43.0 fL_RNAseq

description: Sample 5


title: M1W

description: manual dissection embryo 1


title: 44.4 fL_RNAseq

description: Sample 4


title: M1R

description: manual dissection embryo 1

value: mature Organiser


title: IDH MUT glioma cells treated with DMSO, Replicate 3

description: IDH MUT DMSO


title: 40.1 fL_RNAseq

description: Sample 3


title: M3R

description: manual dissection embryo 3


title: IDH WT glioma cells treated with ATRA, Replicate 3

description: IDH WT ATRA

source_name: IDH WT primary glioma cells

value: IDH WT


title: IDH MUT glioma cells treated with DMSO, Replicate 1

description: IDH MUT DMSO


title: 39.1 fL_RNAseq

description: Sample 2


title: IDH WT glioma cells treated with ATRA, Replicate 2

description: IDH WT ATRA


title: CK-72

city: Zhenjiang

first: Qian

last: xin

state: Jiangsu

address: 301 Xuefu Road

country: China

institute: Jiangsu University

data_processing:
Raw reads were pre-processed to obtain the clean reads by removing reads containing ploy-N, reads containing adapter and low-quality reads from raw data were filtered with FASTQ-Quality-Filter tool.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then, the number of fragments per kilobase of transcript per Million fragments mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: txt files

organism: Rhodotorula mucilaginosa

source_name: Rhodotorula mucilaginosa grown in Nutrient yeast dextrose broth medium

growth_protocol: Nutrient yeast dextrose broth medium (180 rpm) at 28°C

extract_protocol:
The sample was ground in liquid nitrogen.Extraction of total RNA from Rhodotorula mucilaginosm by fungal RNA Extraction Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rhodotorula mucilaginosa strain

value: 15 hours


title: 39.7 fL_RNAseq

description: Sample 1


title: TNP-LPS IgM+ B cells 2

status: Public on Dec 10 2019

city: Valdeolmos

first: Pedro

last: Perdiguero

state: Madrid

address: Ctra. de Algete a El Casar Km 8.1

department: Animal Health Research Centre

country: Spain

institute: CISA-INIA

description: TNP-LPS

data_processing:
Raw sequence reads which passed Illumina quality controls were demultiplexed and adaptor trimmed using the Illumina pipeline
Mapping was performed using TopHat software ( –i 50 and --b2-very-sensitive and --no-coverage-search)
Total reads counts for each gene was merged using Samtools and HTSeq for python
Read count normalization and differential expression analysis was performed using DESeq software (DEGs p value FDR < 0.05)
Genome_build: O. mykiss genome; http://www.genoscope.cns.fr
Supplementary_files_format_and_content: Results from differential expression analysis using DESeq in comparison between KLH_versus_Control, LPS_versus_Control and LPS_versus_KLH

organism: Oncorhynchus mykiss

source_name: Splenic Leukocytes

growth_protocol: Healthy specimens of female rainbow trout (Oncorhynchus mykiss) of approximately 50-70 g were obtained from Centro de Acuicultura El Molino (Madrid, Spain). Fish were maintained at the Animal Health Research Center (CISA-INIA) laboratory at 16ºC with a re-circulating water system and 12:12 h light:dark photoperiod. Fish were fed twice a day with a commercial diet (Skretting, Spain). Prior to any experimental procedure, fish were acclimatized to laboratory conditions for 2 weeks and during this period no clinical signs were ever observed

extract_protocol:
RNAeasy micro kit (Qiagen)
Truseq stranded total RNA kit (Illumina)

treatment_protocol: Leukocytes cultures stimulated with TNP-LPS or TNP-KLH (5 mg/ml) for 24 h

tag: weight

value: Spleen

value: FACS isolated splenic IgM+ B cells


title: IDH WT glioma cells treated with DMSO, Replicate 3

description: IDH WT DMSO


title: TNP-LPS IgM+ B cells 1

description: TNP-LPS


title: TNP-KLH IgM+ B cells 2

description: TNP-KLH


title: TNP-KLH IgM+ B cells 1

description: TNP-KLH


title: TNP-LPS IgM+ B cells 3

description: TNP-LPS


title: Unstimulated IgM+ B cells 3

description: unstimulated


title: TNP-KLH IgM+ B cells 3

description: TNP-KLH


title: Unstimulated IgM+ B cells 1

description: unstimulated


title: PAT-Y

source_name: Rhodotorula mucilaginosa induced by patulin and then grown in Nutrient yeast dextrose broth medium


title: SJWK9

city: Shanghai

first: Wei-Lin

last: JIN

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: Bulk RNAseq_LUAD brain met6

data_processing:
Reads in fastq files from bulk RNA sequecing were first aligned to human genome reference GRCh38 with Hisat2, and then gene expression counts were calculated with Stringtie.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression counts

source_name: Lung adenocarcinoma

extract_protocol:
RNA extraction protocolnot provided.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: surgical resected metastatic brain tissue

tag: metastasis site

value: brain

value: Lung adenocarcinoma

tag: Sex

value: male


title: SJWK6

description: Bulk RNAseq_LUAD brain met4

value: female


title: Regnase_1_null_rep2

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description: JWR132_1554180_ClariomSmouse.rma-gene-full-Signal

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: sgRNA transduced OT-I cells from the B16-Ova melanoma-bearing mice

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain background

value: sgRNA transduced OT-I cells

tag: genotype/variation


title: Batf/Regnase_1_null_rep3

description: JWR137_1554185_ClariomSmouse.rma-gene-full-Signal

value: Batf/Regnase1 null


title: IDH WT glioma cells treated with ATRA, Replicate 1

description: IDH WT ATRA

value: primary glioma cells


title: Batf/Regnase_1_null_rep1

description: JWR135_1554183_ClariomSmouse.rma-gene-full-Signal


title: Regnase_1_null_rep1

description: JWR131_1554179_ClariomSmouse.rma-gene-full-Signal


title: Batf/Regnase_1_null_rep2

description: JWR136_1554184_ClariomSmouse.rma-gene-full-Signal


title: SJWK4

description: Bulk RNAseq_LUAD brain met2

tag: age


title: SJWK5

description: Bulk RNAseq_LUAD brain met3


title: SJWK1

description: Bulk RNAseq_LUAD brain met1


title: IDH WT glioma cells treated with DMSO, Replicate 2

description: IDH WT DMSO


title: plate3

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

description: single-cell FACS sorted for INS, GCG, SST, or none

data_processing:
base-calling Illumina BaseSpace pipeline Paired-end sequencing for both bulk and single-cell samples. Bulk samples are separated by sample, single-cell samples are separated by plate, but all reads are 'Unassigned'.
extract valid reads (single-cell) custom Python script Well barcode and UMI are extracted from the R1 read (well barcode and UMI only) and attached to the read name of the corresponding R2 read (mRNA sequence). Reads with invalid well barcodes are discarded. The resulting 'valid' sequence reads for each plate are processed as single-ended.
align to hg19 genome tophat v2.0.14 aligned to hg19 with default parameters.
(bulk) align transcripts and quantification RSEM 1.2.29 aligned using default parameters (RefSeq annotations)
(single-cell) align transcripts and quantification ESAT v1.0 The transcript annotation file contains all RefSeq transcripts with IDs starting with 'NM_', and includes annotation for T cell constant region genes TRAC, TRBC2, TRDC, TRGC1, and TRGC2.
Genome_build: hg19
Supplementary_files_format_and_content: (bulk) <sample>.xlsx Excel file column A: gene symbol, column B: transcript ID, column C: estmated count in transcripts per million (TPM)
Supplementary_files_format_and_content: (single-cell) <plateID>.umi.txt text file column 1: gene symbol, remaining columns: raw observed transcript count for each gene for the well. The well bacrode for each well is mapped to the plate well in the plateBarcodeMap.txt file.
Supplementary_files_format_and_content: (single-cell) FACS output text file column 1: plate ID, column 2: Well ID, column 3: FACS stort status (INS, GCG, SST, Neg, or Bad)

source_name: recovered endocrine cells plate #3

growth_protocol: samples whose names end in “rec” were cultured as grafts in mouse renal subcapsular space for 4-5 weeks.

extract_protocol:
Proteinase K digestion followed by purification of nucleic acids using Agencourt RNAclean XP beads, DNase digestion and purification of RNA using Agencourt RNAClean XP beads.
bulk RNA-Seq: SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (Takara Bio USA, Mountain View, CA, USA)
single cell: SCRB-Seq

value: recovered endocrine


title: 16083_beta_rec

description: bulk RNA-Seq

source_name: recovered beta cells #3

value: pancreatic beta


title: plate2

source_name: recovered endocrine cells plate #2


title: plate1

source_name: recovered endocrine cells plate #1


title: Regnase_1_null_rep4

description: JWR134_1554182_ClariomSmouse.rma-gene-full-Signal


title: 15306_beta_rec

description: bulk RNA-Seq

source_name: recovered beta cells #2


title: Unstimulated IgM+ B cells 2

description: unstimulated


title: 16083_alpha_rec

description: bulk RNA-Seq

source_name: recovered alpha cells #3

value: pancreatic alpha


title: 16083_alpha_pre

description: bulk RNA-Seq

source_name: pre-engraftment alpha cells #3


title: IDH WT glioma cells treated with DMSO, Replicate 1

description: IDH WT DMSO

value: DMSO


title: SJWK8

description: Bulk RNAseq_LUAD brain met5


title: 15306_alpha_rec

description: bulk RNA-Seq

source_name: recovered alpha cells #2


title: 15306_alpha_pre

description: bulk RNA-Seq

source_name: pre-engraftment alpha cells #2


title: 15306_beta_pre

description: bulk RNA-Seq

source_name: pre-engraftment beta cells #2


title: 15275_beta_rec

description: bulk RNA-Seq

source_name: recovered beta cells #1


title: 15275_alpha_rec

description: bulk RNA-Seq

source_name: recovered alpha cells #1


title: 15275_beta_pre

description: bulk RNA-Seq

source_name: pre-engraftment beta cells #1


title: MS19270_PBMC

first: Chenling

last: Xu

address: Stanley Hall

data_processing:
Raw bcl files were de-multiplexed using cellranger v2.0.2 mkfastq
Subsequent read alignments and transcript counting was done individually for each sample using cellranger count with standard parameters.
Cellranger aggr was employed, to ensure that all samples had the same number of confidently mapped reads per cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Standard cellranger output format

source_name: peripheral blood mononuclear cell

extract_protocol:
Patient Inclusion Criterior: 1) treatment naive patients with a first episode suggestive of MS (i.e. clinically isolated syndrome (CIS)) or with relapsing-remitting (RR)MS diagnosed based on MAGNIMS criteria86, 2) patients receiving LP for diagnostic purposes and consenting to participate.
Patient Exclusion Criterior: 1) questionable diagnosis of MS by clinical signs or magnetic resonance imaging (MRI) findings, 2) secondary chronic progressive MS or primary progressive MS. IIH patients were included, if they gave informed consent. Exclusion criteria for all patients were: 1) immunologically relevant co-morbidities (e.g. rheumatologic diseases), 2) severe concomitant infectious diseases (e.g. HIV, meningitis, encephalitis), 3) pregnancy or breastfeeding, 4) younger than 18 years, 5) mental illness impairing the ability to give informed consent, 6) artificial blood contamination during the lumbar puncture resulting in >200 red blood cells / μl.
Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2
AMPure beads (Beckman Coulter)
 Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup

tag: disease condition

value: Multiple Sclerosis


title: PST95809_PBMC

value: idiopathic intracranial hypertension


title: PTC85037_PBMC


title: PTC32190_PBMC


title: PTC85037_CSF

source_name: Cerebrospinal fluid


title: MS60249_PBMC


title: PST83775_PBMC


title: PTC41540_PBMC


title: MS74594_PBMC


title: MS71658_PBMC


title: 16083_beta_pre

description: bulk RNA-Seq

source_name: pre-engraftment beta cells #3


title: PTC41540_CSF


title: MS49131_PBMC


title: PTC32190_CSF


title: MS74594_CSF


title: MS60249_CSF


title: PST83775_CSF


title: MS71658_CSF


title: MS49131_CSF


title: MS19270_CSF


title: MS58637_CSF


title: PST95809_CSF


title: C10 Normal E+P+TPA

city: Chicago

first: Julie

last: Kim

state: IL

address: 303 E. Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Normal E+P+TPA

growth_protocol: 28 day

extract_protocol:
Direct-zol RNA microprep kit.
standard oligo-dT Illumina TruSeq kits

tag: patient id

tag: patient's age

tag: cancer

tag: menopause

value: pre

tag: length of e treatment

value: 28 days

tag: length of p +/- tpa treatment

value: 14 days (TPA added when P added at day 14)

value: Mammary gland


title: C9 Normal E+P+TPA

value: No

tag: tissue


title: C8 Normal E+P+TPA

value: NO


title: C13 Normal E+P+TPA


title: PTC45044_CSF

institute: UC Berkeley


title: B14 Normal E+P

source_name: Normal E+P


title: C5 BRCA E+P+TPA

source_name: BRCA E+P+TPA


title: B13 Normal E+P


title: C7 BRCA E+P+TPA


title: B8 Normal E+P


title: C3 BRCA E+P+TPA

value: L DCIS


title: C1 BRCA E+P+TPA


title: C2 BRCA E+P+TPA


title: B12 Normal E+P


title: B5 BRCA E+P

source_name: BRCA E+P


title: B2 BRCA E+P


title: B7 BRCA E+P


title: B3 BRCA E+P


title: B9 Normal E+P


title: C14 Normal E+P+TPA


title: C6 BRCA E+P+TPA


title: B1 BRCA E+P


title: B6 BRCA E+P


title: B10 Normal E+P


title: C12 Normal E+P+TPA


title: S120.FF.Pi.0806T1

city: Chapel Hill

first: Xianlu

middle: Laura

last: Peng

state: NC

address: 450 West Dr.

institute: The University of North Carolina at Chapel Hill

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 Conversion Software 2.20.0.
Individual lane files were combined into one FASTQ for each sample
FASTQ of PDX samples were split into human and mouse reads using bbmap v37.90
The total expected read counts per gene were quantified by Salmon 0.9.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: PrimaryPDAC

extract_protocol:
RNA and DNA was harvested from FFPE samples using the Roche High Pure RNA Paraffin Kit (CAT#3270289001) following manufacturer's instructions. RNA and DNA was harvested from FF and FNA samples using the Qiagen AllPrep DNA/RNA Mini Kit (CAT#80204) following manufacturer's instructions.
Libraries were constructed from FFPE and FNA samples using the Illumina TruSeq RNA Exome Library Prep Kit (CAT#20020189,#20020490,#20020492,#20020493,#20020183) following manufacturer's instructions. Libraries were constructed from FF samples using the Illumina TruSeq Stranded mRNA Kit (CAT#20020595,#20019792) following manufacturer's instructions.

tag: sample type

value: FF

tag: lib prep kit

value: TruSeq

tag: extraction protocol

value: Qiagen AllPrep DNA/RNA Mini Kit


title: S121.FF.Pi.0806T1


title: S123.FF.Pi.0608T1


title: S122.FF.Pi.0121T1


title: S118.FF.Pi.0417T1


title: S124.FF.Pi.1207T1


title: S119.FF.Pi.0424T1


title: S116.FF.Pi.1205T1


title: S115.FF.Pi.1204T1


title: S117.FF.Pi.0129T1


title: S113.FF.Pi.1009T1


title: S114.FF.Pi.1119T1


title: S111.FF.Pi.0711T1


title: S109.FF.Pi.0614T1


title: S106.FF.Pi.0524T1


title: S105.FF.Pi.0523T1


title: S104.FF.Pi.0523T1


title: S102.FF.Pi.0502T2


title: S103.FF.Pi.0508T1


title: S108.FF.Pi.0607T1


title: S100.FF.Pi.0417T1


title: S125.FF.Pi.PancT6


title: S098.FF.Pi.0328T1


title: 15275_alpha_pre

description: bulk RNA-Seq

source_name: pre-engraftment alpha cells #1

tag: cell type


title: S099.FF.Pi.0411T1


title: S097.FF.Pi.0327T1


title: S101.FF.Pi.0425T1


title: S090.FF.Pi.1109T1


title: S096.FF.Pi.0222T1


title: S091.FF.Pi.1129T1


title: S092.FF.Pi.1206T1


title: S088.FF.Pi.0417T1


title: S089.FF.Pi.0503T1


title: S112.FF.Pi.0904T1


title: S107.FF.Pi.0605T1


title: S084.FF.Pi.1012T1


title: S086.FF.Pi.0105T1


title: S082.FF.Pi.0517T1


title: S085.FF.Pi.1118T1


title: S095.FF.Pi.0221T1


title: S087.FF.Pi.0119T1


title: S078.FFPE.Pi.0806T1


title: S083.FF.Pi.0818T1


title: S094.FF.Pi.0124T1


title: S110.FF.Pi.0710T2


title: S075.FFPE.Pi.0503T1


title: S076.FFPE.Pi.0417T1


title: S080.FF.Pi.0825T1


title: S079.FF.Pi.0422T1


title: S073.FF.PDX.PancT6

source_name: PDX


title: S071.FF.PDX.1112T1


title: S072.FF.PDX.1125T2


title: S081.FF.Pi.1119T1


title: S074.FFPE.Pi.0517T1


title: S093.FF.Pi.1214T1


title: S070.FF.PDX.0902T1B


title: S068.FF.PDX.0806T1


title: S069.FF.PDX.0508T1


title: S067.FF.PDX.1109T1


title: S063.FF.PDX.0119T1


title: S066.FF.PDX.0616T1


title: S064.FF.PDX.0218T2


title: S065.FF.PDX.0225T1


title: S062.FF.PDX.0319T1


title: S060.FF.PDX.0411T1


title: S059.FF.PDX.1108T1


title: S061.FF.PDX.0523T1


title: S057.FF.PDX.0113T1


title: S055.FFPE.PDX.0910T1

value: FFPE

value: TruSeq RNA Exome

value: Roche High Pure RNA Paraffin Kit


title: S056.FF.PDX.1222T1


title: S058.FF.PDX.1108T1


title: S049.FFPE.PDX.1222T1


title: S050.FFPE.PDX.0113T1


title: S054.FFPE.PDX.0417T1


title: S048.FNA.PDX.0902T1B

value: FNA


title: S051.FFPE.PDX.1108T1


title: S053.FFPE.PDX.1109T1


title: S046.FNA.PDX.0616T1


title: S047.FNA.PDX.0508T1


title: S045.FNA.Pi.1207T1


title: S044.FNA.Pi.0608T1


title: S052.FFPE.PDX.1109T1


title: S040.FNA.Pi.0417T1


title: S042.FNA.Pi.0806T1


title: S041.FNA.Pi.0424T1


title: S043.FNA.Pi.0121T1


title: S036.FNA.Pi.1119T1


title: S038.FNA.Pi.1205T1


title: S039.FNA.Pi.0129T1


title: S037.FNA.Pi.1204T1


title: S035.FNA.Pi.1009T1


title: S034.FNA.Pi.0904T1


title: S032.FNA.Pi.0710T2


title: S033.FNA.Pi.0711T1


title: S029.FNA.Pi.0605T1


title: S031.FNA.Pi.0614T1


title: S027.FNA.Pi.0523T1


title: S028.FNA.Pi.0524T1


title: S026.FNA.Pi.0508T1


title: S022.FNA.Pi.0411T1


title: S021.FNA.Pi.0328T1


title: S024.FNA.Pi.0425T1


title: S023.FNA.Pi.0417T1


title: S025.FNA.Pi.0502T2


title: S019.FNA.Pi.0222T1


title: S018.FNA.Pi.0221T1


title: S020.FNA.Pi.0327T1


title: S015.FNA.Pi.1206T1


title: S016.FNA.Pi.1214T1


title: S012.FNA.Pi.0921T1


title: S011.FNA.Pi.0503T1


title: S014.FNA.Pi.1129T1


title: S013.FNA.Pi.1109T1


title: S010.FNA.Pi.0417T1


title: S007.FNA.Pi.1118T1


title: S009.FNA.Pi.0119T1


title: S008.FNA.Pi.0105T1


title: S005.FNA.Pi.0818T1


title: S006.FNA.Pi.1012T1


title: S030.FNA.Pi.0607T1


title: S003.FNA.Pi.1119T1


title: S002.FNA.Pi.0825T1


title: S004.FNA.Pi.0517T1


title: cut and run sample2 plusplus5

data_processing:
Library strategy: CUT&RUN
Quality trimming: trimmomatic v0.32: paired-end reads removed where average quality scores in window size=10 are <15, bases trimmed where leading and trailing quality scores <15
Length filtering: bedtools v2.25.0: Reads longer than 25 bases after trimming are used for analysis
Alignment to hg19 genome: bowtie2 v2.2.3: option: --un-conc to filter out non-concordant reads
Duplicate removal: MarkDuplicates v0.32: from Picard package
Peak calling: MACS2:
Convert aligned reads to tdf files: IGVTools v2.3.31: for visualization in IGV
Genome_build: hg19

source_name: blood

extract_protocol: Cleavage Under Targets and Release Using Nuclease (CUT&RUN)

value: PBMCs

value: blood

tag: population

value: CD36+, CD56hi


title: S001.FNA.Pi.0422T1


title: cut and run sample2 plusplus4


title: S017.FNA.Pi.0124T1


title: cut and run sample2 plusplus2


title: cut and run sample2 plusplus1


title: cut and run sample2 plusplus3


title: cut and run sample2 plus5

value: CD36+, CD56dim


title: cut and run sample2 plus4


title: cut and run sample2 plus1


title: cut and run sample2 plus3


title: cut and run sample2 plus2


title: cut and run sample2 plusplus0


title: cut and run sample2 minus5

value: CD36-, CD56dim


title: cut and run sample2 plus0


title: cut and run sample2 minus1


title: cut and run sample2 minus3


title: cut and run sample2 minus4


title: cut and run sample1 plusplus5


title: cut and run sample1 plusplus4


title: cut and run sample1 plusplus0


title: cut and run sample1 plus3


title: cut and run sample1 plus5


title: cut and run sample1 plus2


title: cut and run sample1 plus0


title: cut and run sample1 plus1


title: cut and run sample1 minus5