title: Liver_high-fat-diet_control_biological-rep3

city: Kingston

first: Marisa

last: Pfohl

state: RI

address: Pharmacy Building, 7 Greenhouse Road

department: BPS

institute: University of Rhode Island

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing:
Command Console CHP file version 1: rma-gene-full.chp
data was analyzed using Transcriptome Analysis Console software, default cutoff values: p-value ≤ 0.5, FC = ≤ -2 or ≥ 2

source_name: liver tissue from mouse administered a high fat diet (45%kCal from fat) for 12 weeks

label_protocol: Affymetrix

growth_protocol: mice were 6 weeks old at the start of the experiment and were sacrified at 18 weeks of age

extract_protocol: liver RNA was extracted using Trizol according to the manufacturer's protocol

treatment_protocol: mice were administered dietary intervention ad libitum for 12 weeks

tag: diet

value: high-fat-diet

tag: agent

value: control

tag: tissue

value: liver

tag: gender

value: male


title: Liver_high-fat-diet_MSX_biological-rep2

status: Public on May 21 2019

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: liver tissue from mouse administered a high fat diet (45%kCal from fat) containing maple syrup extract (0.5% w/w) for 12 weeks

value: MSX

tag: strain


title: Liver_high-fat-diet_MSX_biological-rep1


title: Liver_high-fat-diet_MSX_biological-rep3


title: Liver_high-fat-diet_control_biological-rep1


title: Liver_high-fat-diet_control_biological-rep2


title: Liver_low-fat-diet_MSX_biological-rep3

source_name: liver tissue from mouse administered a low fat diet (10%kCal from fat) containing maple syrup extract (0.5% w/w) for 12 weeks

value: low-fat-diet


title: Liver_low-fat-diet_MSX_biological-rep1


title: Liver_low-fat-diet_MSX_biological-rep2


title: Human fetal liver  (E1_101#748)

type: SRA

city: London

first: Joe

middle: M

last: Segal

address: 28 floor Tower wing, Great Maze pond

department: Centre of Stem Cell and Regenerative Medicine

country: United Kingdom

institute: Kings college London

library_source: transcriptomic

data_processing:
Raw sequencing reads were aligned using STAR and per gene counts were calculated using HTSEQ
Gene counts were further analyzed using the R package SCATER for pre-processing, quality control and normalization
To filter out bad cells from scRNA-seq analysis we used median absolute deviations (MADs) on library size, total genes detected, mitochondrial gene percentage and artificial ERCC spike in percentage. Two deviations from the median were used to remove cell outliers. For library size and total genes the lower tail outliers were excluded. For mitochondrial and ERCC spike in percentage upper tail outliers were excluded.
T-SNE analysis, clustering and gene expression performed in R
Genome_build: GRCh38
Supplementary_files_format_and_content: [Series_count_matrix.csv] Raw HTSEQ counts for all samples and feature date
[Series_feature_matrix.csv]   MetaData including FACS gating population for each sample

organism: Homo sapiens

source_name: Human fetal liver

extract_protocol:
Human fetal tissue was dissociated by Collagenase XI enzymatic dissociation for 25 minutes at 37˚C with agitation. Samples were stained with the following primary antibodies, CD235a (349104, FITC, mouse; Biolegend), CD45 (304050, BV711, mouse; Biolegend), EpCAM (324208, APC, mouse; Biolegend), NCAM (362524, PE, mouse; Biolegend) all at 1:100 dilution and incubated for 30mins at 4˚C. DAPI (D1306, ThermoFisher Scientific) at 1:1000 dilution was used for live/dead staining.  Cells were sorted using a BD FACS Aria II instrument and deposited as single cells into 96-well plates, pre-loaded with lysis buffer (1% Triton X-100, 1mM dNTP, 1μM oligo-dT30, 1:1.2x106 ERCC ExFold RNA spike-in, Recombinant RNase Inhibitor (2313B, Takara Clontech). Single-cell sequencing was performed using SmartSeq2.
RNA was converted into cDNA using SMARTScribe Reverse Transcriptase (639538, Takara Clontech) and amplified for 21 cycles (Kapa HiFi HotStart ReadyMix 2x, KK2602, KAPA Biosystems). Successful single cell libraries were identified by capillary gel electrophoresis (DNF-474-1000, High Sensitivity NGS Fragment Analysis Kit, AATI) and converted into sequencing libraries using a Nextera XT DNA Sample Preparation Kit (FC-131-1096, Illumina). Barcoded libraries were pooled and subjected to 75 base pair paired-end sequencing on a Illumina HiSeq 2500 instrument.

tag: sample type

value: Freshly isolated human fetal liver homegenate

tag: sample id

value: Human fetal liver 2

tag: Sex

value: Unknown

tag: age

value: 16 postconceptional weeks (pcw)

tag: developmental stage

value: fetal


title: Human fetal liver  (E10_101#887)


title: Human fetal liver  (D7_101#653)


title: Liver_low-fat-diet_control_biological-rep3

source_name: liver tissue from mouse administered a low fat diet (10%kCal from fat) for 12 weeks


title: Human fetal liver  (D8_101#669)


title: Human fetal liver  (D9_101#684)


title: SAM24336973 Bone Marrow Parental

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. G
ene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is
similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supple
mentary files use Entrez Gene IDs, counts and nRPKM statistics.

molecule: polyA RNA

source_name: RNA from wildtype and Irf2 knock out HOXB-8 cell lines

extract_protocol:
Total RNA was extracted from control Luc gRNA iMACs and Irf2 gRNA2 KO iMAC lines (n=3) using a RNeasy Kit (QIAGEN)
with on-column DNase digestion. QC of total RNA was done to determine sample quantity and quality. The concentration of RNA was determined using NanoDrop 8000 (Thermo Scientific)
and the integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies). 100 ng of total RNA was used as an input material for library preparation using
TruSeq Stranded Total RNA Library Prep Kit (Illumina).

value: Bone Marrow

tag: group

value: Parental


title: SAM24336983 Bone Marrow IRF2_KO


title: Human fetal liver  (D6_101#639)


title: Human fetal liver  (D4_101#606)


title: SAM24336982 Bone Marrow IRF2_KO


title: Liver_low-fat-diet_control_biological-rep1


title: Human fetal liver  (D5_101#623)


title: SAM24336974 Bone Marrow Parental


title: b6_spret_lcmv_cd8_d07_scRNAseq

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

country: China

institute: SJTU

description: scRNA-seq

data_processing:
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align ChIP-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ChIP-seq duplicates: Picard v1.141
Call ChIP-seq peaks: MACS2 v2.1.1
Genome_build: GRCm38, CAST/EiJ and SPRET/EiJ
Supplementary_files_format_and_content: *_ATACseq.atlas.cnt: Peak abundance measurements.
Supplementary_files_format_and_content: *_RNAseq.gene.cnt, scRNAseq.cnt.csv: Gene abundance measurements.
Supplementary_files_format_and_content: *.pks.txt: ChIP-seq peaks.

source_name: B6/Spret F1 Spleen activated CD8 T cell

extract_protocol: Chromium™ Single Cell 3' Reagent Kit (v2).

value: B6/Spret F1

value: Spleen

tag: cell type

value: Activated CD8 T cell

tag: time point


title: b6_cast_lcmv_cd8_d07_chip_bkg_tbet

description: processed data: b6_cast_lcmv_cd8_d07_chip_tbet.pks.txt

library_source: genomic

molecule: genomic DNA

source_name: B6/Cast F1 Spleen activated CD8 T cell

extract_protocol:
Kapa Hyper Prep Kit.
Qiagen MinElute PCR purification kit.

value: B6/Cast F1


title: Human fetal liver  (E11_101#902)


title: SAM24336984 Bone Marrow IRF2_KO


title: b6_cast_lcmv_cd8_d07_chip_r2_tbet


title: b6_cast_lcmv_cd8_d07_chip_r4_tbet


title: SAM24336975 Bone Marrow Parental


title: b6_cast_lcmv_cd8_d07_chip_r2_eomes

description: processed data: b6_cast_lcmv_cd8_d07_chip_eomes.pks.txt


title: Human fetal liver  (D1_101#560)


title: Human fetal liver  (C9_101#495)


title: Human fetal liver  (D2_101#576)


title: b6_cast_lcmv_cd8_d07_chip_bkg_eomes


title: Human fetal liver  (D11_101#715)


title: b6_cast_lcmv_cd8_d07_chip_r5_cbfb

description: processed data: b6_cast_lcmv_cd8_d07_chip_cbfb.pks.txt


title: Liver_low-fat-diet_control_biological-rep2


title: Human fetal liver  (C4_101#415)


title: b6_cast_lcmv_cd8_d07_chip_r4_cbfb


title: Human fetal liver  (C7_101#463)


title: Human fetal liver  (C6_101#446)


title: b6_cast_lcmv_cd8_d07_chip_r3_cbfb


title: Human fetal liver  (C2_101#386)


title: Human fetal liver  (C11_101#528)


title: Human fetal liver  (C12_101#545)


title: Human fetal liver  (C10_101#511)


title: b6_cast_lcmv_cd8_nav_chip_bkg_cbfb

description: processed data: b6_cast_lcmv_cd8_nav_chip_cbfb.pks.txt

source_name: B6/Cast F1 Spleen naïve CD8 T cell

value: Naive CD8 T cell


title: Human fetal liver  (D10_101#700)


title: b6_cast_lcmv_cd8_d07_chip_r1_cbfb


title: b6_cast_lcmv_cd8_d07_chip_r3_eomes


title: Human fetal liver  (C1_101#372)


title: b6_cast_lcmv_cd8_nav_chip_r3_cbfb


title: Human fetal liver  (C8_101#480)


title: Human fetal liver  (B9_101#305)


title: b6_cast_lcmv_cd8_d07_chip_bkg_cbfb


title: Human fetal liver  (B8_101#289)


title: Human fetal liver  (B7_101#272)


title: SL39392: ILC2s_SI_SS

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequences were mapped to the murine genome (mm10) STAR aligner; only a single-end from paired-end samples were used
HTSeq-count was used to map reads to mm10 genes
DESeq2 was used to normalize gene expression quantification
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized gene quantification and differential expression analysis, note: processed data for each sample is as indicated in the characteristic: processed DESeq2 RLOG counts and characteristic: processed DESeq2 differential analysis

extract_protocol:
Cells were lysed and snap-frozen in trizol, thawed for chloroform extraction and loaded onto a Qiagen RNEasy column
Libraries were constructed using Protocol 1 (poly-A selection, NEBNext Ultra II Directional RNA Library Prep, TruSeq SR 51bp) or Protocol 2 (Nugen Ovation RNAseq System V2 and Nugen Ovation Ultralow Library System), as indicated in the characteristic: RNA library protocol

treatment_protocol: Innate lymphoid cells were sorted from SI or LI lamina propria at steady state or 3.5-4 days following citrobacter rodentia infection

value: innate lymphoid cells of the small intestine (SI)

tag: genotype

value: WT

tag: treatment

value: steady state

tag: rna library protocol

value: Protocol 2

tag: processed deseq2 normalized counts

tag: processed deseq2 differential analysis results


title: Human fetal liver  (D3_101#592)


title: Human fetal liver  (B6_101#257)


title: Human fetal liver  (B5_101#241)


title: Human fetal liver  (B3_101#212)


title: SL39396: ILC2s_LI_SS

value: innate lymphoid cells of the large intestine (LI)


title: SL39395: CCR6-ILC3s_SI_SS


title: SL39403: CCR6-ILC3s_LI_4DPI_citro

value: 4 DPI citrobacter rodentia


title: Human fetal liver  (B12_101#354)

value: Freshly isolated human fetal liver homegenate

value: Human fetal liver 2


title: Human fetal liver  (B11_101#337)

value: Unknown

value: 16 postconceptional weeks (pcw)


title: Human fetal liver  (B10_101#320)

value: fetal


title: 14_CCTCGG: NK_SILP_4

source_name: NK


title: b6_cast_lcmv_cd8_nav_chip_r2_cbfb


title: 12_TTCAGC: ILC3_CCR6n_SILP_3


title: 11_GGACCC: ILC1_SILP_3


title: Human fetal liver  (A7_101#93)


title: Human fetal liver  (A8_101#107)


title: 10_CCTTCA: NK_SILP_3


title: Human fetal liver  (A6_101#76)


title: 13_AAGACG: ILC3_CCR6p_SILP_3


title: 9_AAGGGA: ILC3_CCR6n_LILP_Citro_d3.5_2


title: 7_GGATGT: ILC2_LILP_Citro_d3.5_2


title: Human fetal liver  (A4_101#45)


title: 6_CCTCGG: ILC3_CCR6n_LILP_1


title: 15_GGATGT: ILC1_SILP_4


title: Human fetal liver  (A12_101#168)


title: Human fetal liver  (A9_101#120)


title: 4_TTCAGC: ILC2_LILP_1


title: Human fetal liver  (A11_101#152)


title: 2_CCTTCA: ILC3_CCR6p_SILP_2


title: Human fetal liver  (A10_101#135)


title: Human fetal liver  (A1_101#1)


title: 8_TTCGCT: ILC3_CCR6p_LILP_Citro_d3.5_2


title: SNW24: ILC3_CCR6pos_Bcl6_KO_3

value: Bcl6-F/F Ncr-Cre+/-

value: Protocol 1


title: Human fetal liver  (A5_101#62)


title: Human fetal liver  (A3_101#29)


title: 1_AAGGGA: ILC2_SILP_2


title: SNW23: ILC3_CCR6pos_Bcl6_KO_2


title: Human fetal liver  (H8_102#1381)


title: Human fetal liver  (H7_102#1365)


title: SNW22: ILC3_CCR6pos_Bcl6_KO_1


title: Human fetal liver  (A2_101#14)


title: 5_AAGACG: ILC3_CCR6p_LILP_1


title: Human fetal liver  (H4_102#1320)


title: SNW19: ILC3_CCR6pos_WT_1


title: SNW20: ILC3_CCR6pos_WT_2


title: Human fetal liver  (H3_102#1304)


title: SNW18: ILC3_CCR6neg_Bcl6_KO_3


title: SNW17: ILC3_CCR6neg_Bcl6_KO_2


title: Human fetal liver  (H10_102#1412)


title: SNW16: ILC3_CCR6neg_Bcl6_KO_1


title: Human fetal liver  (H1_102#1276)


title: SNW15: ILC3_CCR6neg_WT_3


title: SNW21: ILC3_CCR6pos_WT_3


title: SNW14: ILC3_CCR6neg_WT_2


title: Human fetal liver  (G8_102#1227)


title: Human fetal liver  (G7_102#1214)


title: SNW12: ILC1_Bcl6_KO_3


title: SNW13: ILC3_CCR6neg_WT_1


title: Human fetal liver  (G6_102#1197)


title: Human fetal liver  (G5_102#1183)


title: Human fetal liver  (G4_102#1168)


title: SNW11: ILC1_Bcl6_KO_2


title: SNW10: ILC1_Bcl6_KO_1


title: Human fetal liver  (G2_102#1137)


title: SNW9: ILC1_WT_3


title: Human fetal liver  (G3_102#1152)


title: SNW8: ILC1_WT_2


title: SNW7: ILC1_WT_1


title: Human fetal liver  (G12_102#1272)


title: Human fetal liver  (G11_102#1270)


title: Human fetal liver  (G9_102#1241)


title: SNW6: NK_Bcl6_KO_3


title: SNW4: NK_Bcl6_KO_1


title: Human fetal liver  (G10_102#1254)


title: Human fetal liver  (F9_102#1056)


title: SNW5: NK_Bcl6_KO_2


title: Human fetal liver  (F8_102#1040)


title: SL39394: CCR6+ILC3s_SI_SS


title: SNW1: NK_WT_1


title: Human fetal liver  (F6_102#1007)


title: Human fetal liver  (F7_102#1023)


title: SNW2: NK_WT_2


title: SNW3: NK_WT_3


title: 122314_SI_ILC3_CCR6neg_AGGCAGAA: CCR6-ILC3_SI_3

description: accessible DNA

data_processing:
Sequences were mapped to the murine genome (mm10) with bowtie2 v2.2.3
Sequences were filtered (MAPQ>30) with Samtools
Duplicates were removed using Picard
Peakdeck (parameters -bin 75, -STEP 25, -back 10000, -npBack 100000) was used to call peaks (Praw < 1E-4)
A reference set of peaks was found by taking the union of peaks across samples
HTSeq-count was used to map reads to reference peaks
DESeq2 was used to quantify peak accessibility across samples and test for differential accessibility
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized (RLOG) quantification for ATAC-seq peaks, peak annotations (nearest TSS, transcription factor motifs found within the peak, etc.)

source_name: CCR6-ILC3 from SI

extract_protocol:
Cells harvest was followed by a transposition reaction and purification (Buenrostro  et al. Curr Protoc Mol Biol. 2015)
Prepared as in Buenrostro  et al. Curr Protoc Mol Biol. 2015

treatment_protocol: Innate lymphoid cells were sorted from SI or LI lamina propria

value: wild type


title: 122314_SI_ExILC3_CGTACTAG: exILC3_SI_3

description: accessible DNA

source_name: exILC3 from SI


title: Human fetal liver  (F5_102#996)


title: 122314_LI_ILC3_CCR6pos_CAGAGAGG: CCR6+ILC3+LI_3

description: accessible DNA

source_name: CCR6+ILC3 from LI


title: Human fetal liver  (F2_102#951)


title: Human fetal liver  (F4_102#979)


title: Human fetal liver  (G1_102#1121)


title: b6_cast_lcmv_cd8_nav_chip_r1_cbfb

value: Spleen


title: Human fetal liver  (F12_102#1104)


title: 122314_LI_ILC3_CCR6neg_CTCTCTAC: CCR6-ILC3_LI_3

description: accessible DNA

source_name: CCR6-ILC3 from LI


title: 122314_SI_ILC3_CCR6pos_TCCTGAGC: CCR6+ILC3_SI_3

description: accessible DNA

source_name: CCR6+ILC3 from SI


title: Human fetal liver  (D12_101#732)


title: b6_cast_lcmv_cd8_d07_chip_r1_eomes

value: B6/Cast F1

value: Activated CD8 T cell


title: Human fetal liver  (F10_102#1071)


title: 121314_SI_ILC1_TAAGGCGA: ILC1_SI_3

description: accessible DNA

source_name: ILC1 from SI

value: innate lymphoid cells of the small intestine (SI)


title: Human fetal liver  (F11_102#1088)


title: b6_cast_lcmv_cd8_d07_chip_r2_cbfb


title: b6_cast_lcmv_cd8_nav_chip_r4_cbfb

value: Naive CD8 T cell


title: Human fetal liver  (E8_102#857)


title: 121314_LI_ILC1_GGACTCCT: ILC1_LI_3

description: accessible DNA

source_name: ILC1 from LI

value: steady state


title: 020315_SI_ExILC3_CGAGGCTG: exILC3_SI_4

description: accessible DNA


title: Human fetal liver  (B1_101#182)


title: 020315_SI_ILC1_GCTACGCT: ILC1_SI_4

description: accessible DNA


title: Human fetal liver  (E5_102#811)


title: Human fetal liver  (E9_102#873)


title: 2_ILC1_SILP_AGGCAGAA : ILC1_SILP_2

description: accessible DNA


title: 020315_LI_ILC1_AAGAGGCA: ILC1_LI_4

description: accessible DNA


title: Human fetal liver  (E7_102#842)


title: Human fetal liver  (E4_102#795)


title: 020315_LI_ExILC3_GTAGAGGA: exILC3_LI_4

description: accessible DNA

source_name: exILC3 from LI


title: 2_NK_SILP_TCCTGAGC : NK_SILP_2

description: accessible DNA

source_name: NK from SI


title: Human fetal liver  (E3_102#780)


title: Human fetal liver  (E2_102#764)


title: Human fetal liver  (E6_102#826)


title: Human fetal liver  (F1_102#936)


title: Human fetal liver  (E12_102#919)


title: AD13_GTCGTGAT: ILC1_1

description: accessible DNA

source_name: ILC1 and NK from SI


title: AD4_TCCTGAGC: ILC3_CCR6-_2

description: accessible DNA


title: Human fetal liver  (H9_102#1396)

source_name: Human fetal liver


title: Human fetal liver  (D9_102#685)


title: AD14_ACCACTGT: ILC1_2

description: accessible DNA


title: AD3_AGGCAGAA: ILC3_CCR6-_1

description: accessible DNA


title: 1_ILC1_SILP_TAAGGCGA: ILC1_SILP_1

description: accessible DNA


title: 1_NK_SILP_CGTACTAG : NK_SILP_1

description: accessible DNA


title: AD2_CGTACTAG: ILC3_CCR6+_2

description: accessible DNA


title: AD6_TAGGCATG: ILC2_2

description: accessible DNA

source_name: ILC2 from SI


title: AD5_GGACTCCT: ILC2_1

description: accessible DNA


title: Human fetal liver  (E11_102#903)


title: Human fetal liver  (D6_102#640)


title: rnaseq_ssc3_JQ1

city: Baltimore

first: Joseph

middle: Y

last: Shin

state: MD

address: 733 N Broadway MRB-539

institute: Johns Hopkins University School of Medicine

description: normalized_counts_rnaseq_dmsojq1_MERGE.txt

data_processing:
ATAC-seq: basecalling was performed using CASAVA. Reads were trimmed for adapter sequences, and aligned to UCSC hg19 using bowtie2. Duplicate fragments were identified and removed using PICARD tools. Reads were filtered for alignment quality greater than Q30. Reads that mapped to mitochondria, unmapped contigs, or the Y chromosome were removed. Sequence reads were subsequently filtered for nucleosome-free reads based on read fragment size limits (0 to 100 bp), which were determined previously (Buenrostro JD et al. 2013. Nature. 10:1213-8). Peaks were called using MACS2
RNA-seq: bascalling was performed using CASAVA. RSEM was used to align reads to UCSC hg19 and to generate gene expression levels. Count output from RSEM was used as input for DESeq2 differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: bigwig files. RNA-seq (first set): tab-delimited text containing normalized read couts.

source_name: dermal fibroblasts

growth_protocol: Primary dermal fibroblasts lines were established from skin biopsies taken from healthy control donors or patients with diffuse cutaneous SSc. Fibroblasts were cultured at 70-80% confluency in DMEM + 10% FCS + anti/anti + glutamax, and subjected to ATAC-seq and RNA-seq. For treatment studies, fibroblasts were treated with DMSO or JQ1 prior to RNA isolation.

extract_protocol:
Chromatin lysates were isolated upon centrifugation after cell-lysis. RNA was isolated by trizol and RNA isolation columns.
ATAC-seq: Nuclei were isolated from three control and three SSc fibroblast lines using ATAC lysis buffer, transposed with Tn5 transposase (Illumina) for 30 minutes, and ligated with barcoded adapter sequences as previously described (Buenrostro JD et al. 2013. Nature. 10:1213-8). Library quantitation and quality check was performed using an Agilent 2100 Bioanalyzer prior to sequencing as previously described, and 50 base-pair paired-end FASTQ reads were generated by Illumina HiSeq 2000. RNA-seq: RNA was isolated from three control and three SSc fibroblast lines using Trizol and RNeasy isolation kit (Qiagen). DNA was digest with on-column DNase treatment (Qiagen). The quality of the RNA used for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples had RNA integrin numbers (RIN) of at least 9.60. mRNA was enriched by poly-A selection, prepped using an Illumina TruSeq mRNA sample preparation kit, and sequenced by Illumina HiSeq 2000.

treatment_protocol: Control and SSc fibroblasts were treated with DMSO or JQ1 (0.25 uM) for 48 hours in complete cell culture media.

tag: passage

tag: disease state

value: diffuse SSc

value: JQ1 treatment

value: dermal fibroblasts


title: Human fetal liver  (E10_102#888)

value: Freshly isolated human fetal liver homegenate


title: rnaseq_ssc2_JQ1


title: rnaseq_ssc1_JQ1


title: rnaseq_control2_JQ1

value: healthy control


title: Human fetal liver  (D3_102#593)

value: Human fetal liver 2

value: Unknown


title: Human fetal liver  (D8_102#670)

value: 16 postconceptional weeks (pcw)

value: fetal


title: rnaseq_control3_JQ1


title: Human fetal liver  (D7_102#654)


title: AD1_TAAGGCGA: ILC3_CCR6+_1

description: accessible DNA

tag: tissue


title: Human fetal liver  (D4_102#607)


title: Human fetal liver  (D11_102#716)


title: Human fetal liver  (D1_102#561)


title: Human fetal liver  (D2_102#577)


title: Human fetal liver  (D10_102#701)


title: rnaseq_ssc3_DMSO

value: DMSO


title: rnaseq_ssc2_DMSO


title: Human fetal liver  (D12_102#733)


title: rnaseq_ssc1_DMSO


title: Human fetal liver  (C8_102#481)


title: Human fetal liver  (C7_102#464)


title: Human fetal liver  (C9_102#496)


title: rnaseq_control1_JQ1


title: Human fetal liver  (C6_102#447)


title: Human fetal liver  (D5_102#624)


title: Human fetal liver  (H2_102#1290)


title: Human fetal liver  (C5_102#432)


title: rnaseq_ssc3


title: rnaseq_control1_DMSO


title: Human fetal liver  (C4_102#416)


title: Human fetal liver  (C3_102#401)


title: rnaseq_control3


title: rnaseq_ssc1


title: rnaseq_ssc2


title: rnaseq_control2


title: 3_GGACCC: ILC3_CCR6n_SILP_2

tag: strain

value: WT

value: Protocol 2


title: rnaseq_control3_DMSO


title: Human fetal liver  (B2_101#197)

tag: sample type


title: rnaseq_control2_DMSO


title: Human fetal liver  (C10_102#512)

tag: sample id


title: Human fetal liver  (C1_102#373)

tag: Sex


title: nucleosome_free_ssc3

source_name: dermal fibroblasts - nucleosome free


title: nucleosome_free_ssc2


title: rnaseq_control1


title: Human fetal liver  (C12_102#546)

tag: age


title: nucleosome_free_ssc1

data_processing:
ATAC-seq: basecalling was performed using CASAVA. Reads were trimmed for adapter sequences, and aligned to UCSC hg19 using bowtie2. Duplicate fragments were identified and removed using PICARD tools. Reads were filtered for alignment quality greater than Q30. Reads that mapped to mitochondria, unmapped contigs, or the Y chromosome were removed. Sequence reads were subsequently filtered for nucleosome-free reads based on read fragment size limits (0 to 100 bp), which were determined previously (Buenrostro JD et al. 2013. Nature. 10:1213-8). Peaks were called using MACS2
RNA-seq: bascalling was performed using CASAVA. RSEM was used to align reads to UCSC hg19 and to generate gene expression levels. Count output from RSEM was used as input for DESeq2 differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: bigwig files. RNA-seq : tab-delimited text containing normalized read couts.

treatment_protocol:
For ATAC-seq: No treatment protocol.Sequencing performed on cells cultured at baseline conditions.
For RNA-seq (set#1) : No treatment protocol. Sequencing performed on cells cultured at baseline conditions.
For RNA-seq (set#2) : Control and SSc fibroblasts were treated with DMSO or JQ1 (0.25 uM) for 48 hours in complete cell culture media.

value: DMSO or JQ1 treatment for RNA-seq (set #2)


title: nucleosome_free_control2


title: Human fetal liver  (B8_102#290)

tag: developmental stage


title: Human fetal liver  (B7_102#273)


title: Human fetal liver  (B6_102#258)


title: nucleosome_free_control1

treatment_protocol: ATAC-seq: No treatment. Sequencing performed on cells cultured at baseline conditions. RNA-seq (set#1) : No treatment. Sequencing performed on cells cultured at baseline conditions.. RNA-seq (set#2) : Control and SSc fibroblasts were treated with DMSO or JQ1 (0.25 uM) for 48 hours in complete cell culture media.


title: Human fetal liver  (B5_102#242)


title: Human fetal liver  (C2_102#387)


title: Human fetal liver  (H5_102#1335)


title: Human fetal liver  (B4_102#228)


title: Human fetal liver  (B11_102#338)


title: Human fetal liver  (B10_102#321)


title: Human fetal liver  (B12_102#355)


title: Human fetal liver  (B3_102#213)


title: Human fetal liver  (B2_102#198)


title: Human fetal liver  (A9_102#121)


title: Human fetal liver  (A8_102#108)


title: Human fetal liver  (B9_102#306)


title: Human fetal liver  (C11_102#529)


title: Human fetal liver  (A6_102#77)


title: Human fetal liver  (A7_102#94)


title: Human fetal liver  (A3_102#30)


title: Human fetal liver  (A4_102#46)


title: Human fetal liver  (A5_102#63)


title: Human fetal liver  (A2_102#15)


title: Human fetal liver  (A12_102#169)


title: Human fetal liver  (B1_102#183)


title: Human fetal liver  (A1_102#2)


title: Human fetal liver  (A11_102#153)


title: Human fetal liver  (A10_102#136)


title: 9-GC-MB-6586_S9

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

data_processing:
Genomic mapping was performed by the Genomics Centre using Fastq files aligned to HG 19 using STAR aligner implemented in BaseSpace (RNA-Seq Alignment pipeline v 1.1.0, Illumina).
BAM file outputs from STAR were annotated using Partek Genomic Suite (v6.6) and the RefSeq data base (RefSeq 21).
Differential analysis was performed with Partek Genomic Suite (v6.6) running ANOVA.
Genome_build: hg19
Supplementary_files_format_and_content: cyber

source_name: HFFF2 human foreskin primary fibroblasts

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
total RNA was extracted using TRIzol Reagent. First strand cDNA synthesis was performed with SuperScript III First-Strand Synthesis System. After purification using SPRI beads, the double stranded cDNA was ligated to in-house designed adapters (based on TruSeq Indexed adapters (Illumina)) using NEBNext Ultra II (NEB) followed by 15 cycles of amplification and library purification

tag: type


title: 8-GC-MB-6586_S8


title: 11-GC-MB-6586_S11


title: 5-GC-MB-6586_S5


title: 7-GC-MB-6586_S7


title: 10-GC-MB-6586_S10


title: 4-GC-MB-6586_S4


title: 6-GC-MB-6586_S6


title: 12-GC-MB-6586_S12


title: 2-GC-MB-6586_S2


title: 3-GC-MB-6586_S3


title: 1-GC-MB-6586_S1


title: 34+ 235a+ 41a+ hematopoietic progenitor cells+ expanded in HSC expansion conditions with UM171 for 5 days

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 1 --seed-length 25 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: human embryonic stem cells (h1ESCs)-derived hematopoietic progenitors

growth_protocol: Human embryonic stem cells (h1ESCs) generated in this study were directed to differentiate towards hematopoietic progenitors on collagen IV-coated plate in xeno-free condition using stage-wise cytokine combinations as is described in Uenish et al.

extract_protocol:
RNAs were isolated using RNeasy Mini Kit (Qiagen) from cell population of interest
Samples were then prepared for sequencing using the Ligation Mediated Sequencing (LM-Seq) protocol

treatment_protocol: Hematopoietic progenitors from day 9 chemically defined feeder free differentiation cultures were expanded in HSC expansion conditions, for 16 hrs or 5 days,  with DMSO or UM171 (35 nM)


title: 34+ 235a+ 41a+ hematopoietic progenitor cells+ expanded in HSC expansion conditions with DMSO for 5 days


title: 34+ 235a+ 41a+ hematopoietic progenitor cells+ expanded in HSC expansion conditions with DMSO for 16 hrs


title: 34+ 235a+ 41a+ hematopoietic progenitor cells+ expanded in HSC expansion conditions with UM171 for 16 hrs


title: HiC in CAPH2 KD, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Reads were separately aligned to the human genome (hg19) using bowtie2. Redundant paired reads derived from a PCR bias, reads aligned to repetitive sequences, and reads with low mapping quality (MapQ < 30) were removed. Reads potentially derived from self-ligation and undigested products were also discarded.  Hi-C biases in contact maps were corrected using the ICE method with 30 iterations.
Genome_build: hg19
Supplementary_files_format_and_content: ICE normalized interaction matrix for 1MB resolution

extract_protocol:
In situ Hi-C was performed as previously described (Rao et al., 2014, Cell)
Sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc).
in situ HiC

tag: cell line

value: KD


title: HiC in CAPH2 KD, replicate 2


title: HiC in ARID1A KO, replicate 2

source_name: RMG1_ARID1A CRISPR

value: KO


title: HiC in ARID1A KO, replicate 1


title: HiC in ARID1A/CAPH2 WT


title: CHIP-seq of SNF5 in ARID1A WT cells

data_processing:
CHIP-seq data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files
Genome_build: hg19
Supplementary_files_format_and_content: CHIP-seq signal in bigwig format

source_name: RMG1 cell line

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. The reaction was quenched by 0.125 M glycine for 5 min. Fixed cells were lysated with ChIP lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, pH8.0, 1% Triton X-100, 0.1% DOC) on ice and lysis buffer 2 (10 mM Tris pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at room temperature. Chromatin was digested with MNase (Cell Signaling) in digestion buffer (10 mM Tris 8.0, 1 mM CaCl2, 0.2% Triton X-100) at 37°C for 15 min. The nucleus was broken down by one pulse of bioruptor with high output. Chromatin were incubated overnight at 4°C and protein A+G Dynabeads were added to the reaction for another 1.5 hour. Magnetic beads were washed and chromatin was eluted. Eluted DNA was treated with proteinase K at 55°C for 45 min and decrosslinked at 65°C overnight. Zymo ChIP DNA clean and concentrator kit (zymo, cat. no. D5205) was used to purify the ChIP DNA
10 ng ChIP DNA was used for library construction. NEBNext Ultra DNA Library Prep Kit (NEB, E7645) was used to prepare sequencing library

tag: factor

tag: chip antibody

value: rabbit anti-SNF5 (Bethyl, cat. no. A301-087A)


title: CHIP-seq of SNF5 in ARID1A KO cells

source_name: RMG1 cell line, ARID1A CRISPR


title: CHIP-seq of H3K4me3 in ARID1A KO cells

value: rabbit anti-H3K4me3 (Active Motif, cat. no. 39159)


title: CHIP-seq input in ARID1A KO cells

description: CHIP.input.KO

value: input

value: none (input)


title: CHIP-seq of H3K4me3 in ARID1A WT cells


title: CHIP-seq of H3K27ac in ARID1A KO cells

value: rabbit anti-H3K27ac (Abcam, cat. no. ab4729)


title: CHIP-seq of CAPH2 in ARID1A KO cells

value: rabbit anti-CAP-H2 (Bethyl, cat. no. A302-276A)


title: HTG_1

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

description: microRNA derived from liver tissue of high temperature group (LTG) fish

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp).
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: Genome database:Cyprinus carpio:common carp genome (assembly GCF_000951615.1); miRbase release 21
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

organism: Cyprinus carpio

source_name: liver

growth_protocol: The experimental procedures used in this study were approved by the Institutional Animal Care and Use Committee of Sichuan Agricultural University. Ninety fish were randomly divided into three tanks (30 fish in each). For cool and heat stress, all fish were subjected to a stepped cooling regime of 1℃/h for a maximum of 7℃/day and warming by the same regime. The fish were cooled from 17℃ to 5℃ and acclimated at 5℃ was named low temperature group (LTG), the other fish were warmed from 17℃ to 30℃ and acclimated at 30℃ was named high temperature group (HTG), and control group (CG) was maintained at 17℃. The fish were sampled after acclimated 18 days.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: Sampled after fasting for two days, the fish were anesthetized with MS-222. Their livers were collected from three groups in each five fish and immediately snap-frozen in liquid nitrogen, stored at -80℃ until use.

tag: group

value: high temperature group

value: liver


title: CHIP-seq of CAPH2 in ARID1A WT cells


title: HTG_2


title: CG_2

description: microRNA derived from liver tissue of control (LTG) fish

value: control group


title: HTG_3


title: CG_1


title: CHIP-seq of ARID1A in ARID1A WT cells

value: rabbit anti-ARID1A (Abcam, cat. no. ab182560)


title: CHIP-seq of H3K27ac in ARID1A WT cells


title: LTG_3

description: microRNA derived from liver tissue of low temperature group (LTG) fish

value: low temperature group


title: RNA-seq in CAPH2 KD cells, replicate 2

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.12 software was used to estimate raw read counts using Ensemble transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains raw counts for each gene

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) according to the manufacturer's instruction and digested with DNase I (Qiagen, 79254) and purified using RNeasy MinElute Cleanup Kit (Qiagen, 74106)
RNA-Seq libraries were prepared using TruSeq Total RNA Sample Prep Kit (Illumina)


title: LTG_1


title: LTG_2


title: CHIP-seq input in ARID1A WT cells

description: CHIP.input.wt


title: RNA-seq in CAPH2 KD cells, replicate 1


title: ChIP_combined

first: Qin

last: Shen

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

description: ChIPed-DNA, pooled by different biological duplicates

data_processing:
Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
The sequencing reads (fastq format) for input and ChIP libraries were mapped to GRCm38 genome assembly using the bowtie2 program allowing for up to 1 mismatching in seed alignment. The mapping files (SAM format) were fed into MACS2 software with default parameters for peak calling. For visualization, the bedGraph files were generated and normalized using the log10 likelihood ratio method implemented in MACS2, which were then converted to bigwig format using the “bedGraphToBigWig” function in UCSC tools.
Genome_build: GRCm38 genome
Supplementary_files_format_and_content: The peaks.txt file contains information about called peaks; The narrowPeak is BED format file which include the peak location, peak summit, pvalue and qvalue; The BigWig format files ending with ".bw" can be loaded as custom track in UCSC genome browser, which present the signal of ChIP-seq experiments.

source_name: E14.5 mouse forebrain cortex

extract_protocol:
ChIP protocols were modified from previously described (Shen et al., 2009). DNA from two replicates was mixed and sent for library construction and sequencing.
ChIP samples were quantified using a Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and qualified by Agilent Bioanalyzer 2100(Agilent Technologies, Palo Alto, CA, USA). Next generation sequencing library preparations were constructed following the manufacturer’s protocol (NEBNext® Ultra™II DNA Library Prep Kit for Illumina®). For each sample, at least 10 ng ChIP product was used for library preparation. The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor-ligated DNA was then recovered using AxyPrep Mag PCR Clean-up (Axygen). Each sample was then amplified by PCR for 8 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer. Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

treatment_protocol: Tissues of the dorsal cortices were dissected from E14.5 embryonic mouse and digested into single cell using papain solution. Then these cells were used for following normal ChIP processes.

value: forebrain cortex

tag: cell type

value: dissociated primary cortical cells

value: ICR

value: ZEB1 (Santa Cruz Biotechnologies, Cat.No.sc25388)


title: Input_combined

description: input DNA,pooled by different biological duplicates


title: E14.5-16.5 OE-r2

description: sorted GFP+ cells that have been electroporated with CAG-Zeb1-IRES-ZsGreen plasmid

data_processing:
Zebra call(base calling software developed for BGISEQ-500) software was used for basecalling.
Sequenced reads were trimmed using SOAPnuke software to get clean data.
Sequences of the clean data were mapped to the mouse reference genome (version GRCm38) from ensemble databases with STAR (Dobin et al., 2013) using default parameters. The read counts for each gene (generated by STAR) in each sample were used as input to DESeq2 (Love et al., 2014) for differentially expression analysis.The relative transcript abundances (FPKM, Fragments Per Kilobase of transcript per Million mapped reads) were calculated by Cufflinks（Trapnell et al., 2010).
Submitted raw data files in "fastq" type were clean data from control or overexpression groups from biological duplicates.
Genome_build: GRCm38
Supplementary_files_format_and_content: The file "ALL_FPKM" contains all the FPKM values for each sample.

source_name: E16.5 mouse forebrain cortex

extract_protocol:
E14.5 cortex was in utero electroporated with GFP plasmid (either CAG control or Zeb1-overexpression plasmid) and developed for 48h in utero. Then the cortices were dissected and dissociated with papain to single cells. GFP+ cells were sorted out. Total RNA was extracted with Trizol reagent (Life Technologies, USA, Cat.No.15596018) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the standard BGISEQ-500 protocol.

value: embryonic day 16.5

tag: genotype

value: Zeb1-overexpressing cells


title: RNA-seq in CAPH2 WT cells, replicate 2

value: WT


title: E14.5-16.5 OE-r1


title: CG_3


title: mixture of 8 blood samples

city: wuhan

first: lifang

last: liu

address: HZAU

institute: HZAU

data_processing:
Raw data was checked and filtered with FastQC and fastp (Chen et al., 2018)
The clean data of each sample produced from DGE-seq was mapped to the reference transcriptome assembled before using Bowtie2 program (Langmead, Salzberg, 2012).
Gene expression levels were estimated using FPKM values (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced).
The read counts of each sample were imported into the R package NOISeq25 for the differential expression analysis.
The p value was adjusted using q value (false discovery rate), and q value < 0.05 and |log2 (foldchange)| > 1 were set as the threshold for significantly differential expression.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Megalobrama amblycephala

source_name: blood

extract_protocol:
Blood samples were sampled from the caudal vein using heparinized syringes and placed in 2 mL centrifuge tubes. Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

value: mixture of 8 blood samples


title: RNA-seq in CAPH2 WT cells, replicate 1


title: E14.5-16.5 CAG-r2

description: sorted GFP+ cells that have been electroporated with CAG-IRES-ZsGreen plasmid

value: control cells


title: RNA-seq in ARID1A KO cells, replicate 1

value: KO


title: E14.5-16.5 CAG-r1


title: RNA-seq in ARID1A KO cells, replicate 2


title: nucleosome_free_control3

value: healthy control

tag: treatment

value: dermal fibroblasts


title: RNA-seq in ARID1A WT cells, replicate 2


title: RNA-seq in ARID1A WT cells, replicate 1


title: M_Q_C_2

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

institute: Queen's University Belfast

description:
processed data file: mature_miRNA_expression_matrix.txt
processed data file: isomiR_expression_matrix.txt

data_processing:
Basecalling performed using bcl2fastq v2.17.1.14, no lane splitting, barcode mismatches 0.
Raw reads were concatenated between lanes 1-4 from sequencing data in CLC Genomics Workbench v10.11.
Adapters were trimmed in CLC Genomics Workbench v10.1.1.
Sequences were aligned to miRBase v21 in CLC genomics allowing a maximum of 2 mismatches.
Reads were downsampled to 550,000 mapping to microRNAs using CLC Genomics Workbench v10.1.1.
Genome_build: miRBase v21
Supplementary_files_format_and_content: mature_miRNA_expression_matrix.txt: Tab-delimited text file including mature miRNA counts from each sample.
Supplementary_files_format_and_content: isomiR_expression_matrix.txt: Tab-delimited text file including isomiR counts from each sample.

source_name: Plasma

extract_protocol:
MagnaZol cfRNA Isolation Reagent
QIAseq miRNA

value: Plasma

tag: rna extraction method

value: MagnaZol

tag: small rna library prep kit

value: QIAseq


title: SA-50

city: Beijing

first: Fan

last: Xiaolong

address: No.19,Waida Jie,Xinjie Kou, Haiding District

institute: Beijing Normal University

data_processing:
Raw sds files or eds files generated by 7900HT Fast Real-Time PCR System were imported to  Expression Suite Software v1.0.4 (Thermo Fisher Scientific).
The cycle threshold (CT ) for each gene was automatically determined by  Expression Suite Software v1.0.4 .
CT values  of the classifier genes were normalized against the geometric average CT values of ACTB，GAPDH and UBC.

label: FAM

source_name: Frozen glioma tissue

label_protocol: PCR assays were performed using a custom Taqman Low Density Array (TLDA, Life Technology). Two μl of cDNA template was diluted to 50 μl using RNAse-free water and subsequently mixed with 50 μl 2x TaqMan Universal PCR Master mix with UNG (Life Technology). This reaction mix was then loaded to each slot of the TLDA card. The card was centrifuged twice at 1500 rpm for 1 min to transfer 1 μl of the mix to each reaction cell, sealed and subsequently measured using ABI 7900HT fast real-time PCR system or ViiA™ 7 Flex Real-Time PCR system following the universal cycling conditions: 2 min at 50℃ for UNG incubation and 10 min at 95℃ for polymerase activation. Forty cycles (15 s at 95℃ for denaturation and 1 min at 60℃ for annealing and synthesis) were run for amplification.

extract_protocol: Total RNA was extracted from about 30mg frozen  tissue using AllPrep DNA/RNA Mini Kit (QIAGEN,Cat No./ID: 80204)

tag: histology

value: sGBM

tag: grade

tag: idh mutation

tag: 1p19q co-deletion

value: non co-deletion

tag: em/pm class

value: PM


title: SA-49

tag: gender

value: F

tag: age

value: AO

value: MT

value: co-deletion


title: M_Q_C_1

tag: tissue


title: SA-47

value: GBM

value: EMlowPMlow


title: SA-42

value: M

value: WT


title: SA-43


title: SA-41

value: EM


title: SA-46


title: SA-45


title: SK 20 42h rep3

city: Indianapolis

first: Andy

last: Chen

state: IN

address: 410 W 10th Street, Suite 5000

department: MMGE

institute: IUSM

data_processing:
Base-calling by default HiSeq 4000 settings
Reads mapped to hg38 by STAR (v2.5) using parameter “--outSAMmapqUnique 60”
Features counted by featureCounts (from subread v1.5.3) using parameters “-s 2 -p -Q 10”
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files contain raw counts from featureCounts

source_name: SK-N-BE(2) neuroblastoma

growth_protocol: 1:1 mixture of EMEM and F12K with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
RNA extracted with QIAgen Rneasy, samples prepped with TruSeq RNA Library Pre Kit v2
Libraries prepared according to Illumina protocols for HiSeq 4000

treatment_protocol: 24h and 42h incubation with 10 mM and 20 mM ethanol

value: 20 mM ethanol

tag: timepoint

value: brain

tag: cell line

value: neuroblastoma

value: male

value: 2 years


title: SK 20 42h rep4


title: SA-44


title: SA-48


title: M_Q_B_2

value: Plasma

value: MagnaZol

value: QIAseq


title: SA-39

value: F

value: non co-deletion


title: SA-40


title: SA-38

value: AOA

value: MT

value: PM


title: M_Q_B_1


title: SK 20 42h rep1


title: SK 10 42h rep4

value: 10 mM ethanol


title: M_Q_A_1


title: SK 20 42h rep2


title: M_NF_C_1

extract_protocol:
MagnaZol cfRNA Isolation Reagent
NEXTflex Small RNA v3

value: NEXTflex


title: DLD1 siUHRF1-1

type: genomic

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description:
9992576093_R01C01_Grn.idat
9992576093_R01C01_Red.idat
DLD1 with UHRF1 siRNA1 plus mock
DLD1-siUHRF1-1

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
BeadStudio software V2011.1
Signals were background subtracted and normalized to internal controls using GenomeStudio V2011.1 and Methylation Module 1.9.0.

label: Cy5 and Cy3

source_name: DLD1 with UHRF1 siRNA1 plus mock

label_protocol: Standard Illumina Protocol

growth_protocol: DLD1 cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Genomic DNA was extracted using the standard phenol-chloroform method.

treatment_protocol: DLD1 cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 48 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h.

tag: sirna

value: UHRF1 siRNA1

value: UHRF1 depletion

tag: agent

value: mock


title: DLD1 siUHRF1-1 plus TSA

description:
9682764154_R05C01_Grn.idat
9682764154_R05C01_Red.idat
DLD1 with UHRF1 siRNA1 plus TSA
DLD1-siUHRF1-1-TSA

source_name: DLD1 with UHRF1 siRNA1 plus TSA

value: Trichostatin A


title: RKO siCONT

description:
3999547139_R05C01_Grn.idat
3999547139_R05C01_Red.idat
RKO with control siRNA plus mock
RKO-siCONT

source_name: RKO with control siRNA plus mock

growth_protocol: RKO cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: RKO cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h.

value: RKO

value: control


title: SA-36

value: GBM

value: WT

value: EM


title: SK 10 42h rep2

value: brain

tag: cell type

value: neuroblastoma

value: male

value: 2 years


title: M_NF_B_2

value: Plasma

value: MagnaZol


title: SA-37

value: F

value: non co-deletion


title: M_NF_C_2

value: NEXTflex


title: SK 10 42h rep1

value: 10 mM ethanol


title: M_Q_A_2

value: QIAseq


title: SA-31


title: SA-35

value: M


title: SA-34

value: PM


title: SA-30


title: SA-33

value: GBM, gliosarcoma

value: EMlowPMlow


title: SA-32

value: GBM

value: WT


title: SA-29


title: SA-26


title: RKO siUHRF1-1 plus TSA

description:
3999547139_R05C01_Grn.idat
3999547139_R05C01_Red.idat
RKO with UHRF1 siRNA1 plus TSA
RKO-siUHRF1-1-TSA

source_name: RKO with UHRF1 siRNA1 plus TSA

value: RKO

value: UHRF1 siRNA1

tag: genotype

value: UHRF1 depletion

value: Trichostatin A


title: SA-28

value: EM


title: SA-27


title: DLD1 siCONT

description:
9682764154_R05C01_Grn.idat
9682764154_R05C01_Red.idat
DLD1 with control siRNA plus mock
DLD1-siCONT

source_name: DLD1 with control siRNA plus mock

value: control

value: mock


title: RKO siUHRF1-1

description:
3999547139_R05C01_Grn.idat
3999547139_R05C01_Red.idat
RKO with UHRF1 siRNA1 plus mock
RKO-siUHRF1-1

source_name: RKO with UHRF1 siRNA1 plus mock


title: SK 0 42h rep4

tag: treatment

value: 0 mM ethanol

value: brain

value: neuroblastoma

value: male

value: 2 years


title: SA-25

value: F

value: non co-deletion


title: SK 0 42h rep3


title: SK 0 42h rep2


title: M_NF_A_2

value: Plasma

tag: rna extraction method

value: MagnaZol

value: NEXTflex


title: M_NF_B_1

tag: small rna library prep kit


title: M_NF_A_1


title: SA-24

value: M

tag: histology

value: A


title: SA-21

value: GBM

tag: grade

value: WT

value: PM


title: SA-20

value: GBM-O

tag: idh mutation

value: EM


title: SA-22

tag: 1p19q co-deletion

value: EMlowPMlow


title: SA-23

tag: em/pm class


title: SK 0 42h rep1

value: 0 mM ethanol

value: brain

tag: gender


title: mCT_C_2

extract_protocol:
miRNeasy Serum/Plasma Kit
CleanTag Small RNA

value: miRNeasy

value: CleanTag


title: mCT_C_1


title: SK 10 42h rep3

value: 10 mM ethanol

value: neuroblastoma

value: male

tag: age

value: 2 years


title: mCT_B_2

tag: tissue

value: Plasma


title: mCT_B_1


title: SK 20 24h rep2

value: 20 mM ethanol

tag: timepoint


title: SA-19

value: M

value: A

value: MT

value: non co-deletion


title: SA-18

value: F

value: GBM

value: WT


title: SA-17

value: AOA

value: EM


title: SK 20 24h rep3

value: brain

tag: cell line


title: SA-16

value: GBM-O

value: PM


title: SK 20 24h rep1

value: neuroblastoma


title: Human blood, CT 14

city: Ancona

first: Tiziana

last: Casoli

address: Via Birarelli 8

department: Scientific Technological Area

country: Italy

institute: INRCA

description: Selective amplification of mtDNA

hyb_protocol: The chips were hybridized for 16 h at 49°C, then washed and stained in Fluidics Station 450 according to the suggested protocol.

scan_protocol: Chips were scanned in Affymetrix GeneChip Scanner 3000 7G and data acquisition was performed using the Affymetrix Genechip Command Console (AGCC) software.

data_processing:
Data analysis was carried out with GSEQ 4.1 with “model type” set at diploid to enable the detection of heteroplasmy and “quality score threshold” set at 3 to provide the best base calling accuracy and rate. The other parameters used by the algorithm were No Signal Threshold= 2, Weak Signal Fold Threshold= 20, Large SNR Threshold= 20, Min Fraction of Calls of Samples = 0.5, Trace Threshold = 1, Sequence Profile Threshold = -0.175.
Homoplasmic and heteroplasmic variants were defined by the software through comparison with the revised Cambridge Reference Sequence (rCRS). Probe Intensity File values were used to calculate the Ratio of Expected Allele (REA) and the heteroplasmy percentage.

source_name: Age-matched control

label_protocol: Total DNA was amplified by means of REPLI-g mitochondrial DNA kit (Qiagen) that contains DNA polymerase, buffers, and reagents for the specific amplification of the mitochondrial genome using Multiple Displacement Amplification (MDA). After purification, DNA was quantified  spectrophotometrically  and Genechip Resequencing array kit (Affymetrix) was employed for fragmentation and labeling.

extract_protocol: Total DNA was extracted using a QIAamp DNA blood mini kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol:
The blood samples used in the study came from 15 PD patients (mean age 78.7 ± 6.1; 8 females), treated with levodopa, and 15 age- and sex-matched controls (mean age 80.9 ± 5.1; 9 females). All participants were of Caucasian ethnicity. The PD patients showed late disease onset (≥ 65 years) and no family history of PD. Exclusion criteria for PD patients were a history of other neurological disorders, a diagnosis of PD as a secondary disease, and PD with atypical disease progression. Exclusion criteria for control subjects were a history of any neurological disease, orthostatic hypotension, cognitive impairment, and parkinsonism.
Controls consisted in volunteers and spouses of the patients and were submitted to the same clinic and neuropsychological assessment as the PD group. Each participant underwent blood withdrawal with sodium citrate as anticoagulant.

tag: disease state

value: CT

value: Whole blood

tag: locomotion mode

tag: adl hierarchy scale


title: Human blood, CT 15

description: Selective amplification of mtDNA


title: SA-15


title: Human blood, CT 13

description: Selective amplification of mtDNA


title: mCT_A_2

value: Plasma

value: miRNeasy

value: CleanTag


title: SK 10 24h rep4

value: 10 mM ethanol

tag: cell type

value: male

value: 2 years


title: SK 20 24h rep4

tag: treatment

value: 20 mM ethanol


title: mCT_A_1

tag: rna extraction method


title: SK 10 24h rep3


title: SK 10 24h rep2


title: Human blood, CT 12

description: Selective amplification of mtDNA


title: Human blood, CT 9

description: Selective amplification of mtDNA


title: SK 10 24h rep1


title: SA-12

value: GBM

value: non co-deletion


title: SK 0 24h rep4

value: 0 mM ethanol


title: mQ_B_1

extract_protocol:
miRNeasy Serum/Plasma Kit
QIAseq miRNA

tag: small rna library prep kit

value: QIAseq


title: Human blood, CT 8

description: Selective amplification of mtDNA


title: mQ_B_2


title: SK 0 24h rep3

value: brain


title: SA-10

value: M

tag: histology

value: WT

value: EM


title: SA-13

tag: grade


title: Human blood, CT 10

description: Selective amplification of mtDNA

value: CT


title: SK 0 24h rep2

value: neuroblastoma


title: Human blood, CT 7

description: Selective amplification of mtDNA

value: Whole blood


title: SA-14

value: GBM-O

tag: idh mutation


title: Human blood, CT 6

description: Selective amplification of mtDNA


title: SA-11

value: F

value: MT

tag: 1p19q co-deletion

value: PM


title: SK 0 24h rep1

value: male

value: 2 years


title: SA-08

value: GBM

tag: em/pm class


title: SA-07

tag: gender

value: non co-deletion


title: Human blood, CT 11

description: Selective amplification of mtDNA


title: mQ_C_2

value: Plasma

value: miRNeasy


title: mQ_C_1

value: QIAseq


title: SA-06

value: M

tag: age


title: Human blood, CT 5

description: Selective amplification of mtDNA

tag: tissue


title: NCOA5/KO-1

city: Guangzhou

first: Jingcai

last: He

address: 13 Shi Liu Gang Avenue

institute: TCM-Integrated Cancer Center of Southern Medical University

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 hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatocellular carcinoma cells

tag: genotype/variation

value: NCOA5 knockout


title: SA-05

value: WT

value: EM


title: mQ_A_2


title: SA-09

value: EMlowPMlow


title: Human blood, CT 3

description: Selective amplification of mtDNA

value: CT

value: Whole blood


title: Human blood, CT 4

description: Selective amplification of mtDNA


title: mNF_B_2

extract_protocol:
miRNeasy Serum/Plasma Kit
NEXTflex Small RNA v3

value: NEXTflex


title: mNF_C_1


title: 500-I-R3

city: Vestec

first: Alexandru

last: Mizeranschi

address: Průmyslová 595

country: Czech Republic

institute: BIOCEV

data_processing:
Reads were mapped using Bowtie2 version 2.2.8 and quality checking was done using Samtools version 1.4, Sambamba v. 0.6.6, Bedtools v. 2.26.0 and FastQC v. 0.11.5
Mapped reads were downsampled to 10 million reads per sample and metrics were collected for unmapped, multi-mapping, single-mapping and optical duplicate reads
Unique reads that map to a single location were retained and further downsampled to 3 million reads per sample
Peak calling was performed with MACS2 v. 2.1.1.20160309 using the following settings: -q 0.1, -m 2 50, --bw 186, -g 12000000
Overlapping peaks were counted using Bedtools' intersect and the three most similar replicates per group were retained for IDR analysis.
Genome_build: SacCer3 R64
Supplementary_files_format_and_content: Narrowpeak files containing peaks called for each corresponding pair of FAIRE and input samples

organism: Saccharomyces cerevisiae

source_name: Yeast colony

growth_protocol: Yeast giant colonies (6 per plate) were grown at 28 °C on GMA (1 % yeast extract, 3 % glycerol, 2 % agar, 1 % ethanol, 10 mM CaCl2, 0.05 % glucose, and 0.002 % uracil) with pH dye indicator bromocresol purple.

extract_protocol:
Cell subpopulations removed using a spatula at 3 days, FAIRE samples (but not input samples) cross-linked with formaldehyde, DNA sheared by sonication, phenol-chloroform extraction carried out to purify DNA fragments
FAIRE and input DNA samples were prepared for sequencing using ThruPLEX reagents (Rubicon Genomics, Ann Arbor, MI). 2-5 ng FAIRE or input control DNA was used as starting material for library preparation. Sequencing was performed on a NextSeq 500 instrument (Illumina, San Diego, CA) with 75 bp single-end reads.

tag: strain

tag: biomass

tag: condition

value: Input


title: WT

tag: cell line

value: wild type


title: mNF_B_1


title: SA-04


title: Human blood, CT 2

description: Selective amplification of mtDNA

tag: disease state

tag: locomotion mode

tag: adl hierarchy scale


title: mQ_A_1

tag: rna extraction method

tag: small rna library prep kit


title: SA-03

value: F

tag: histology

tag: grade


title: mNF_A_2


title: Human blood, CT 1

description: Selective amplification of mtDNA


title: SA-02

value: GBM-O

tag: idh mutation

tag: 1p19q co-deletion


title: Human blood, PD 15

description: Selective amplification of mtDNA

source_name: Parkinson's patient

value: PD


title: 500-F-R2

value: FAIRE


title: 500-I-R2


title: SA-01

tag: gender

value: GBM

value: non co-deletion

tag: em/pm class


title: mNF_A_1

tag: tissue

value: Plasma

value: miRNeasy


title: NBT8-2

source_name: Frozen non timor brain tissue

tag: age

value: TBI


title: Human blood, PD 14

description: Selective amplification of mtDNA


title: 500-F-R3

tag: strain


title: mNF_C_2


title: 500-I-R1

tag: biomass


title: NBT8-1


title: Human blood, PD 13

description: Selective amplification of mtDNA


title: 500-F-R1

tag: condition


title: Im-Rep2

city: New Haven

first: Jun

last: Zhao

state: CT

address: 300 George Street

department: Pathology/Immunology

institute: Yale University

data_processing:
Raw data was processed with Drop-seq tools for alignment and generation of digital expression matrix
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of digital expression matrix

source_name: Lung

extract_protocol:
Naive or immunized (day 35) C57BL/6 mice were injected intravenously with 2.5 ug Alexa 700 conjugated anti-CD45.2 Ab in PBS, and after 7 min, mice were euthanized. For in vitro CD45.2 staining, PECy7 conjugated anti-CD45.2 Ab was used. For isolation of total lung cells, cells were collected after 1 hr digestion in RPMI media supplemented with 5% FCS, 1 mg/ml Collagenase D (Roche), 10 mg/ml DNase I (Sigma) and 0.1 mg/ml Dispase II (Sigma) at 37 C 250 rpm. Homogenates were passed through a cell strainer, and ammonium- chloride-potassium lysing buffer was used. After in vitro staining with PECy7 anti-CD45.2 and Pacific blue anti-CD4 Abs, CD45.2 in vivo neg , CD4 neg   cells were sorted into PBS plus 0.01% BSA. The cells were diluted to concentration of 100 cells/μl and 1 ml aliquots were used as input to the Drop-seq protocol. Cells were processed for Drop-seq within ∼30 min of collection.
The beads were purchased from ChemGenes Corporation, Wilmington MA (catalog number Macosko201110) and the PDMS co-flow microfluidic droplet generation device was generated by Nanoshift, Emeryville CA. The cDNA was generated using Template Switch Oligo and the populations of 5,000 beads (∼150 cells) were separately amplified for 16 cycles of PCR (conditions identical to those previously described) with SMART PCR primer and  PCR products were purified by the addition of 0.6x AMPure XP beads (Beckman Coulter). For each conditions the cells from multiple mice were pooled together. Immunized group consisted of cells from 3 mice and naïve condition consisted of 5 mice. Each sample was collected by Drop-seq. For immunized conditions two 1 ml collections were performed and for naïve mouse one collection was performed. For immunized group the cDNA from an estimated 4000 cells was prepared and tagmented by Nextera XT using 1000 pg of cDNA input, and the custom primers New-P5-SMART-hybrid [3] and Nextera XT primers - N701 and N702 (Illumina). For naïve group, cDNA from an estimated 2000 cells was used as input into the Nextera XT tagmentation with New-P5-SMART-hybrid oligoand N704. The concentration and the quality of libraries was measured with Qubit HS DNA assay and Agilent TapeStation Three libraries were sequenced on the Illumina NextSeq 500 using 2.0 pM in a volume of 1.3 ml HT1, and 2 ml of 0.3 μM Custom Read 1 primer (3) for priming of read 1. Read 1 was 20 bp; read 2 (paired end) was 60 bp.

treatment_protocol: For Immunization: Mice were immunized twice (day 0 a 7) by intranasal administration of heat killed Klebsiella pneumoniae (40 ug/ each time)

value: Lung

value: 3 months

tag: treatment

value: Klebsiella pneumoniae immunized mice day 35 after immunization


title: WT

value: Naïve mouse


title: NBT6

value: EMlowPMlow


title: 100-I-R3


title: Human blood, PD 12

description: Selective amplification of mtDNA

tag: disease state

value: Whole blood


title: Im-Rep1


title: Human blood, PD 11

description: Selective amplification of mtDNA

tag: locomotion mode


title: 100-I-R2

value: Input


title: Human blood, PD 10

description: Selective amplification of mtDNA

tag: adl hierarchy scale


title: 100-F-R3


title: Human blood, PD 9

description: Selective amplification of mtDNA


title: 100-F-R2


title: Human blood, PD 8

description: Selective amplification of mtDNA


title: NBT4


title: NBT5


title: NBT3


title: NBT2


title: 100-I-R1


title: 100-F-R1


title: 20-F-R3

value: 20 mg


title: Human blood, PD 4

description: Selective amplification of mtDNA


title: Human blood, PD 6

description: Selective amplification of mtDNA


title: GU-LGG-24

value: F

value: AO

value: MT

value: co-deletion


title: Human blood, PD 7

description: Selective amplification of mtDNA

value: PD


title: GU-LGG-23

value: M

value: A

value: non co-deletion

value: PM


title: 20-I-R2


title: Human blood, PD 3

description: Selective amplification of mtDNA


title: NBT1

value: TBI


title: 20-F-R2

value: FAIRE


title: GU-LGG-22

value: O


title: 20-I-R1


title: Human blood, PD 2

description: Selective amplification of mtDNA


title: Human blood, PD 1

description: Selective amplification of mtDNA


title: GU-LGG-21


title: 20-F-R1


title: GU-LGG-19

value: Ganglioglioma

value: WT

value: EM


title: 4-I-R3

value: 4 mg

value: Input


title: GU-LGG-27

value: EMlowPMlow


title: 20-I-R3

value: 20 mg


title: GU-LGG-20


title: Human blood, PD 5

description: Selective amplification of mtDNA

value: Whole blood


title: 4-F-R3


title: 4-I-R2


title: GU-LGG-18

value: F

value: AA


title: 4-F-R2


title: 4-I-R1


title: GU-LGG-12

value: AOA

value: MT


title: GU-LGG-13

value: M

value: co-deletion


title: 4-F-R1


title: GU-LGG-15

value: PM


title: Nup155+/- 4

city: Sioux Falls

first: Randolph

middle: S

last: Faustino

state: SD

address: 2301 East 60th Street North

department: Genetics and Genomics

institute: Sanford Research

data_processing:
Raw reads (as *.bam) files were imported for expression analysis into Strand NGS (Agilent Technologies, Santa Clara, CA).
Samples were aligned to the Mus musculus genome (Build mm10) and annotated using RefSeq (Release 80).
Unmatched paired-end reads were filtered out for downstream quality control. These datasets were further refined by removing reads that did not reach a mapping quality above 20, as well as those that did not surpass vendor-established quality control (QC) criteria in Strand NGS
Final QC reads were normalized by DESeq with median of all samples used as baseline.
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression values, with normalized abundance measurements supplied in a matrix table as a text file.

source_name: embryonic stem cells

growth_protocol: Cells were cultured on 0.1% gelatin coated 100 mm dishes grown in 10 ml of GTES medium consisting of 85% Glasgow MEM (GMEM), 15% ES qualified Fetal Bovine Serum (FBS), sodium pyruvate, non-essential amino acids (NEAA), penicillin/streptomycin (PenStrep), β-mercapthoethanol (β-ME) and ESGRO Leukemia Inhibitory Factor (LIF). After initial plating (seeding density at 1.0 x 106 – 1.5 x 106 cells), cells were maintained in culture for 2 - 3 passages, changing GTES media as required. At approximately 80% confluency, cells were passaged by treatment with 5 ml of 0.25% trypsin for 4 min at 37°C. Suspension was centrifuged at 1500 rpm for 4 min, and pellets of cells were either resuspended in GTES media to be re-plated or in PBS prior to RNA extraction.

extract_protocol:
Total RNA was extracted with RNeasy Mini kit according to manufacturer’s protocol (Qiagen, Germantown, MD).
RNA libraries were prepared according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) from 100 ng of total RNA. Briefly, polyA mRNA was purified from total RNA using oligo dT magnetic beads. Purified mRNA was fragmented at 95°C for 8 min and eluted from the beads. Double stranded cDNA was prepared using SuperScript III reverse transcriptase, random primers (Invitrogen, Thermo Fisher Scientific, Waltham, MA) and DNA polymerase I and RNase H. The cDNA ends were repaired and an “A” base added to the 3’ ends. TruSeq paired end index DNA adaptors (Illumina, San Diego, CA) with a single “T” base overhang at the 3’ end were ligated and resulting constructs were purified using AMPure SPRI beads (Agencourt Bioscience, Beverly, MA). The adapter-modified DNA fragments were enriched by 12 cycles of PCR using Illumina TruSeq PCR primers (Illumina, San Diego, CA). The concentration and size distribution of the libraries were determined using an Agilent Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA) and Qubit fluorometry (Invitrogen, Thermo Fisher Scientific, Waltham, MA).

tag: cell line

tag: passages

tag: genotype

value: Nup155+/- exon truncated


title: Nup155+/- 3


title: Nup155+/- 5


title: ATF7ip KO 72 hr 3

city: San Francisco

first: Michael

middle: Robert

last: Waterfield

address: 513 Parnassus Ave MSB S-1076

department: Diabetes Center

institute: UCSF

data_processing:
Illumina libraries were generated from total RNA using the Illumina TruSeq Library Prep Kit and sequenced on the Illumina HiSeq 4000 to a depth of at least 20 million reads.
Sequence alignment was performed using STAR (version 2.4.2a; PMID: 23104886). Mappings were restricted to those that were uniquely assigned to the mouse genome and unique read alignments were used to quantify expression and aggregated on a per-gene basis using the Ensembl (GRCm38.78) annotation.
Differential expressed genes between experimental groups were then determined using DESeq2 (v1.16.1; PMID: 25516281).
Genome_build: mm10

source_name: Lymph nodes and spleen

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and purified using a Qiagen micro column.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T Lymphocytes

value: IL-6/TGFb 72hrs


title: ATF7ip KO 72 hr 1


title: ATF7ip KO 72 hr 2


title: ATF7ip Het 72 hr 3


title: GU-LGG-10

tag: histology

tag: grade

value: WT

value: non co-deletion


title: GU-LGG-09

value: AO

tag: idh mutation

tag: 1p19q co-deletion


title: GU-LGG-11

value: Ganglioglioma

tag: em/pm class


title: GU-LGG-08

tag: gender

value: OA


title: Nup155+/- 1


title: ATF7ip Het 72 hr 2

tag: tissue


title: GU-LGG-07

tag: age


title: WT 4

value: wild type


title: ATF7ip Het 72 hr 1

tag: strain


title: ATF7ip KO 24 hr 3

value: IL-6/TGFb 24hrs


title: WT 5


title: GU-LGG-17

value: O


title: GU-LGG-06


title: GU-LGG-05

value: F

value: AA


title: WT 3


title: GU-LGG-02

value: A


title: GU-LGG-04

value: EMlowPMlow


title: WT 2


title: ATF7ip KO 24 hr 2


title: ATF7ip KO 24 hr 1


title: Nup155+/- 2


title: WT 1


title: ATF7ip Het 24 hr 2


title: ATF7ip Het 24 hr 3


title: GU-LGG-01

value: M


title: S39_G3_PRE

city: Budapest

first: Kinga

last: Nemeth

address: Szentkiralyi street 46

department: Department of Laboratory Medicine

country: Hungary

institute: Semmelweis University

data_processing:
Raw reads were processed by trimming off the 3’ adapter and low-quality bases using cutadapt (http://cutadapt.readthedocs.io/en/stable/guide.html).
The insert sequences and UMI sequences were identified.
Sequences were aligned to miRBase v21 mature miRNA sequences using bowtie algorithm (http://bowtie-bio.sourceforge.net/index.shtml).
For each sample all reads assigned to a particular miRNA ID was counted and the associated UMIs were clustered to count unique molecules. UMI read count were used to calculate differential expression.
Genome_build: miRBase v21
Supplementary_files_format_and_content: .xlsx file, containing UMIs, was generated by Qiagen online primary data analysing tool

source_name: pituitary adenoma patient

extract_protocol:
EDTA-anticoagulated plasma samples were isolated by QIAgen miRNeasy Serum/Plasma Kit
miRNA library was prepared by QIAseq microRNA Library Kit (Qiagen)

value: plasma

tag: sample

value: preoperative


title: ATF7ip Het 24 hr 1

value: T Lymphocytes

tag: treatment


title: S40_G3_POST

value: postoperative


title: ATF7ip KO Naïve 3

value: No Treatment


title: G1017

value: GBM

value: WT

value: non co-deletion

value: EM


title: S38_G3_POST


title: S37_G3_PRE


title: ATF7ip KO Naïve 2


title: ATF7ip KO Naïve 1


title: S35_G3_PRE


title: G0912


title: ATF7ip Het Naïve 2


title: G0921

value: MT

value: PM


title: ATF7ip Het Naïve 3


title: G0919


title: S34_G3_POST


title: ATF7ip Het Naïve 1


title: G0605


title: S32_G2_POST


title: G1221

value: AO

value: co-deletion


title: S33_G3_PRE


title: G0608

value: F

value: Suspicious Glioma


title: S31_G2_PRE


title: ESC_Pol2i_FLV

city: Berkeley

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Library strategy: Micro-C
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
allValidPairs were generated by HiC-Pro package (>2.10 version)
mcool files were converted from allValidPairs by Cooler package
hic file were converted from allValidPairs by Juicer tools
Genome_build: mm10
Supplementary_files_format_and_content: allValidParis file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) strand of first locus, 5) chromosome of second locus, 6) read position of second locus, 7) strand of second locus, 8) DNA fragment lengh, 9) name of first restriction fragment, 10) name of second restiction fragment, 11) mapping quality of first read, 12) mapping quality of second read.
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with mutiple resolutions

growth_protocol: JM8.N4 mouse embryonic stem cells were grown on plates pre-coated with a 0.1% autoclaved gelatin solution (Sigma-Aldrich, G9391) under feeder free condition in knock-out DMEM with 15% FBS and LIF (full recipe: 500 mL DMEM (ThermoFisher#10829018), 6 mL MEM NEAA (ThermoFisher #11140050), 6 mL GlutaMax (ThermoFisher#35050061), 5 mL Penicillin-streptomycin (ThermoFisher #15140122), 4.6 μL 2-mercapoethanol (Sigma-Aldrich M3148), 90 mL fetal bovine serum (HyClone FBS SH30910.03 lot #AXJ47554)). mES cells were fed by replacing half the medium with fresh medium daily and passaged every two days by trypsinization.

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

treatment_protocol: Cells were crosslinked by 1% formaldehyde for 10 min at room temperature. Formaldehyde reaction was quenched by 0.75M Tris. After two times of PBS washes, cells were then crosslinked by 3mM DSG for 45 min at room temperature. After two times of PBS washed, cell pellets were snap frozen or subjected to the following protocols.

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Wild-type with Flavopiridoltreatment


title: G0524

value: M


title: G1122

value: AOA


title: ESC_Pol2i_TRP

value: Wild-type with Tripotolide treatment


title: S29_G2_PRE

value: plasma

value: preoperative


title: S36_G3_POST

value: postoperative


title: S30_G2_POST


title: G0517

value: GBM

value: EMlowPMlow


title: G0913

value: WT

value: non co-deletion


title: S28_G2_POST


title: G0515

value: OA

value: MT

value: PM


title: S27_G2_PRE


title: G0510

value: O

value: co-deletion


title: G0510B


title: S26_G2_POST


title: ESC_WT35

value: embryonic stem cells

value: Wild-type


title: ESC_WT34


title: ESC_Pol2i_WT


title: ESC_WT32


title: ESC_WT37


title: ESC_WT33


title: G0508-2

value: M

value: A

value: EM


title: S25_G2_PRE

value: plasma


title: S24_H2

source_name: healthy individual

value: healthy control


title: G0508-1B

source_name: Frozen glioma tissue

value: AO


title: G0427

value: AA


title: G0508-1


title: S23_H1


title: S22_G1_POST

value: postoperative


title: ESC_WT30


title: G0425

value: F


title: ESC_WT36


title: S21_G1_PRE

value: preoperative


title: G0412

value: non co-deletion


title: S20_G1_POST


title: ESC_WT29


title: S19_G1_PRE


title: G0329-3

value: WT

value: EMlowPMlow


title: ESC_WT28


title: ESC_WT27


title: S18_G1_POST


title: ESC_WT26


title: G0329-1

value: O

value: MT

value: PM


title: ESC_WT25

value: embryonic stem cells

value: Wild-type


title: S16_G1_POST


title: epi2

source_name: Frozen epilepsy tissue

value: epilepsy


title: ESC_WT24


title: ESC_WT31


title: epi1


title: S14_G1_POST


title: S15_G1_PRE


title: ESC_WT23


title: D59

value: M

value: sGBM


title: D59B


title: ESC_WT22


title: D52

value: co-deletion


title: S13_G1_PRE

value: plasma


title: S17_G1_PRE


title: ESC_WT21


title: D46

value: rAA


title: S12_G1_POST

value: postoperative


title: S11_G1_PRE


title: ESC_WT19


title: epi3


title: D38

value: F

value: rGBM


title: ESC_WT20


title: S9_G1_PRE

value: preoperative


title: D36

value: WT

value: non co-deletion

value: EM


title: D24

value: AOA

value: MT


title: S6_G1_POST


title: ESC_WT17

value: embryonic stem cells


title: S5_G1_PRE


title: S4_G1_POST


title: ESC_WT15

value: Wild-type


title: D21

value: AA

value: PM


title: D20

value: A


title: D11


title: ESC_WT14


title: S3_G1_PRE


title: 1594C

value: M


title: ESC_WT12


title: S2_G1_POST

value: plasma


title: ESC_WT13


title: 1594-2


title: 1594A


title: 1594B


title: S10_G1_POST


title: ESC_WT10


title: ESC_WT09


title: S1_G1_PRE


title: ESC_WT18


title: ESC_WT11


title: MLL-AF9_DMSO_9wks_scRNA-seq

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Reads from single-cell RNA-seq libraries were processed in R using the scPipe package to map reads to the transcriptome, demultiplex reads to individual cells and counts reads mapping to each gene.
Low quality cells and non-expressed genes were identified with the scater package and removed prior to analysis.
The cell counts were normalised using the scran package.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene count for each cell; Barcode information for demultiplexing single cells

source_name: MLL-AF9 cells

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO).

extract_protocol:
Viable single cells were sorted on the BD FACSAria III directly into pre-prepared 384 well plates that contained a mixture of oligo (dT) primer, dNTPs and ERCC spike ins, as outlined in the Cel-seq2 protocol.
A modified version of Cel-seq2 was used to generate single cell cDNA libraries. Briefly, the sorted cells were lysed and the primers annealed to the RNA at 65°C. Primers contained a 24bp polyT stretch, a 6bp unique molecular identifier (UMI), a cell-specific 8bp barcode, the 5′ Illumina adaptor and a T7 promoter. Reverse transcription, second strand synthesis and in vitro transcription were performed according to the Cel-seq2 protocol, with the exception of the cDNA cleanup step prior to IVT, whereby the volume of the Agencourt AMPure XP beads (A63880, Beckman Coulter) was 5% of the total volume of beads used in the original protocol. Following IVT, the amplified RNA was fragmented, cleaned up and reverse transcribed with a random hexamer primer containing the sequence complimentary to the 3’ Illumina adaptor. Fragments containing both adaptors were selected for by PCR using TruSeq Small RNA primers (Illumina).

treatment_protocol: MLL-AF9 drug naive parental cells were cultured in methycellulose supplemented with either DMSO or 400nM IBET. Every 7 days, 6 x 10^5 cells were re-plated in fresh methycellulose supplemented with increasing concentrations of IBET (600nM, 800nM and 1000nM) or maintained in DMSO. Once the cells had been exposed to 1000nM of IBET, they were maintained in this concentration for a further 4 weeks.removed from I-BET151 media 4 days prior to isolation.

tag: strain background

tag: tissue source

value: haematopoietic progenitors

value: DMSO for 9 weeks


title: MLL-AF9_1000nM IBET_9wks_scRNA-seq

tag: cell line

value: 1000nM IBET for 9 weeks


title: ESC_WT08


title: MLL-AF9_800nM IBET_scRNA-seq

value: 800nM IBET


title: ESC_WT07


title: MLL-AF9_600nM IBET_scRNA-seq

value: 600nM IBET


title: ESC_WT16


title: 1490A

value: sGBM


title: 1490C

value: non co-deletion


title: ESC_WT06


title: 1594

value: WT


title: MLL-AF9_400nM IBET_scRNA-seq

description:
400nmDMSO_S1
the plate also includes DMSO at 7 days and the other half are the 400nM IBET treatment samples.

value: DMSO and 400nM IBET


title: 1574

value: F

value: GBM

value: EM


title: RKO with AZA

description: RKO treated with 5-aza-2'-deoxycytidine

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

source_name: RKO with AZA

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Invitrogen).

treatment_protocol: RKO cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h. Alternatively, RKO cells were treated with 1 microM 5-aza-2'-deoxycytidine for 72 h.

value: RKO

value: colorectal cancer

tag: sirna

tag: drug


title: ESC_WT05

value: embryonic stem cells

value: Wild-type


title: 1490B

extract_protocol: Total RNA was extracted from about 30mg frozen  tissue using AllPrep DNA/RNA Mini Kit (QIAGEN,Cat No./ID: 80204)

value: M

tag: histology

tag: grade

value: MT

value: PM


title: RKO siUHRF1-1 plus TSA

description: RKO with UHRF1 siRNA1 plus TSA

tag: genotype

value: UHRF1 depletion

value: Trichostatin A


title: RKO siUHRF1-2 plus TSA

description: RKO with UHRF1 siRNA2 plus TSA

source_name: RKO with UHRF1 siRNA2 plus TSA


title: MLL-AF9_1000nM IBET_scRNA-seq

value: haematopoietic progenitors

value: 1000nM IBET


title: 1559

value: GBM-O

tag: idh mutation

tag: 1p19q co-deletion

value: co-deletion

tag: em/pm class


title: Irf8_Empty_ResIBET

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using bwa mem
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed
Peak-calling was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bed files of macs2 peaks

source_name: MLL-AF9 I-BET resistant cells

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO), while MLL-AF9 I-BET sensitive cells were cultured with constant DMSO treatment (0.1%).

extract_protocol:
50000 cells were lysed to isolate nuclei.
Isolated nuclei were then tagmented for 30mins at 37°C. Tagmented DNA was then amplified into the final ATACseq libraries using KAPA HotStart Ready Mix (2x) (KAPA Biosystems). Libraries were size selected from 150-700bps.

treatment_protocol: I-BET151 was used at a final concentration of 1000nM. LSD1i was used at a final concentration of 500nM.

tag: cell phenotype

value: I-BET Resistant

tag: shRNA

value: Empty vector


title: Irf8_OverExpression_ResLSD1i

value: Irf8 OverExpression vector


title: RKO siCONT plus TSA replicate1

description: RKO with control siRNA plus TSA replicate1

value: control


title: 1555

tag: age

value: OA

value: WT

value: non co-deletion

value: EMlowPMlow


title: ESC_WT02

value: embryonic stem cells

value: Wild-type


title: Pu-1_Scrambled_ResLSD1i

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

value: Irf8 Scrambled

tag: treatment

tag: chip antibody

value: PU.1/SPI1(2258S, Cell Signaling)


title: Pu-1_Irf8_shRNA1_ResLSD1i

value: Irf8 shRNA


title: ESC_WT01

tag: cell type

tag: genotype/variation


title: ESC_WT03


title: Irf8_ResLSD1i

tag: strain background

tag: tissue source

value: haematopoietic progenitors

value: anti-Irf8 (5628S, Cell signaling)


title: 1566

tag: gender

value: F

value: AO

value: MT

value: PM


title: 1545

value: M

value: co-deletion


title: Irf8_ResIBET

tag: cell line

value: I-BET Resistant

value: IBET


title: ESC_WT04


title: 1540

tag: histology

value: GBM

value: WT

value: non co-deletion

value: EM


title: Ov_H3K4me3_C1

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
For each condition, peaks were identified using MACS 2.1.1 using a shift-size window of 73 bp, no model, and a p-value threshold < 1e-05.
Identification of differential peaks was done using a in-house script: from all of the peaks called we retained only those peaks with average values above the 50th quintile. Then, we selected peaks with fold changes above 1.5 and FDR < 10%. Statistical significance was calculated using a Limma test.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files, bed file containing differential peaks

source_name: Ovary, Control – Rep 1

extract_protocol:
Immunoprecipitated DNA was purified with Qiagen MinElute kit, and 10 µg of DNA was used for library construction.
Library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina  (E7645)

treatment_protocol: The exposure window was embryonic day E6.5 to E15.5. CD was suspended in olive oil and administered at a dose of 100 μg/kg/day in a volume of 150 μl for each mouse. The control mice were treated with the same volume of oil.

tag: strain

value: Swiss

value: Control

tag: tissue

value: ovary

value: H3K4me3 (Merck Millipore, 07-473)


title: Ov_H3K4me3_C2

source_name: Ovary, Control – Rep 2


title: 1542

value: GBM-O

tag: grade

tag: idh mutation


title: Ov_H3K4me3_K2

source_name: Ovary, Chlordecone – Rep 2

value: Chlordecone


title: RKO siUHRF1-2

description: RKO with UHRF1 siRNA2 plus mock

source_name: RKO with UHRF1 siRNA2 plus mock

value: RKO

value: colorectal cancer

tag: sirna

tag: genotype

value: UHRF1 depletion

tag: drug

value: mock


title: Ov_H3K4me3_K1

source_name: Ovary, Chlordecone – Rep 1


title: cast_lcmv_cd8_d07_r3_RNAseq

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

data_processing:
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align ChIP-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ChIP-seq duplicates: Picard v1.141
Call ChIP-seq peaks: MACS2 v2.1.1
Genome_build: GRCm38, CAST/EiJ and SPRET/EiJ
Supplementary_files_format_and_content: *_ATACseq.atlas.cnt: Peak abundance measurements.
Supplementary_files_format_and_content: *_RNAseq.gene.cnt, scRNAseq.cnt.csv: Gene abundance measurements.
Supplementary_files_format_and_content: *.pks.txt: ChIP-seq peaks.

source_name: BMC F1 Spleen Cast activated CD8 T cell

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit followed by KAPA Hyper Prep Kit.
Cells were collected in Trizol and RNA was extracted using RNeasy mini kit.

value: Cast

value: Spleen

value: Activated CD8 T cell

tag: time point


title: LSD1_Res_stLSD1i

value: haematopoietic progenitors

tag: cell phenotype

value: I-BET Resistant

tag: shRNA

tag: treatment

value: KDM1A/LSD1 (ab17721, Abcam)


title: H3K4me2_Scrambled_LSD1i

value: Pu.1 Scrambled

tag: chip antibody

value: anti-H3K4me2 (ab32356, Abcam)


title: 1537

value: M

tag: age

value: GBM

value: WT

tag: 1p19q co-deletion

value: non co-deletion

tag: em/pm class

value: EM


title: H3K4me2_Scrambled_DMSO

tag: strain background

tag: tissue source

tag: cell line

value: DMSO


title: 1534

tag: gender

value: F

tag: histology

value: GBM-O

value: MT

value: PM


title: LSD1_Res

value: IBET


title: RKO siCONT plus TSA replicate2

description: RKO with control siRNA plus TSA replicate2

value: RKO

tag: cell type

value: colorectal cancer

value: control

value: Trichostatin A


title: cast_lcmv_cd8_d07_r2_RNAseq

tag: strain

value: Cast

tag: tissue

value: Spleen

value: Activated CD8 T cell


title: cast_lcmv_cd8_d07_r1_RNAseq


title: 1533

value: AOA

tag: grade

tag: idh mutation


title: H3K4me2_Pu-1_shRNA2_LSDi

value: haematopoietic progenitors

tag: cell phenotype

value: I-BET Resistant

value: Pu.1 shRNA2

value: anti-H3K4me2 (ab32356, Abcam)


title: RKO siCONT replicate1

description: RKO with control siRNA plus mock replicate1

tag: sirna

tag: genotype

tag: drug

value: mock


title: 1521

value: F

tag: age

value: GBM

value: WT

value: non co-deletion

value: EM


title: 1518

value: AO

value: MT

tag: 1p19q co-deletion

value: PM


title: 1508

value: M

tag: em/pm class

value: EMlowPMlow


title: 1514

value: GBM-O


title: H3K4me2_Pu-1_shRNA2_DMSO

tag: strain background

tag: shRNA

tag: treatment

value: DMSO

tag: chip antibody


title: DLD1 siUHRF1-1 plus TSA

description:
DLD1 with UHRF1 siRNA1 plus TSA
DLD1-siUHRF1-1-TSA

source_name: DLD1 with UHRF1 siRNA1 plus TSA

tag: cell line

value: UHRF1 siRNA1

value: UHRF1 depletion

tag: agent

value: Trichostatin A


title: cast_lcmv_cd8_nav_r3_RNAseq

source_name: BMC F1 Spleen Cast naïve CD8 T cell

tag: strain

value: Cast

value: Spleen

tag: cell type

value: Naive CD8 T cell


title: RKO siCONT replicate2

description: RKO with control siRNA plus mock replicate2

value: RKO

value: colorectal cancer

value: control

value: mock


title: RKO siUHRF1-1

description: RKO with UHRF1 siRNA1 plus mock

source_name: RKO with UHRF1 siRNA1 plus mock


title: 1503

tag: gender

tag: histology

value: GBM

tag: grade

value: WT

value: non co-deletion

value: EM


title: DLD1 siUHRF1-2 plus TSA

description:
DLD1 with UHRF1 siRNA2 plus TSA
DLD1-siUHRF1-2-TSA

source_name: DLD1 with UHRF1 siRNA2 plus TSA

tag: sirna

value: UHRF1 siRNA2


title: H3K4me2_Pu-1_shRNA1_DMSO

tag: tissue source

value: haematopoietic progenitors

tag: cell phenotype

value: I-BET Resistant

value: Pu.1 shRNA1

value: anti-H3K4me2 (ab32356, Abcam)


title: H3K4me2_Pu-1_shRNA1_LSD1i


title: cast_lcmv_cd8_nav_r2_RNAseq

tag: tissue


title: cast_lcmv_cd8_nav_r1_RNAseq


title: b6_lcmv_cd8_d07_r2_RNAseq

source_name: BMC F1 Spleen B6 activated CD8 T cell

value: Activated CD8 T cell

tag: time point


title: 1501

source_name: Frozen glioma tissue

value: M

tag: age

tag: idh mutation

tag: 1p19q co-deletion

tag: em/pm class

value: EMlowPMlow


title: H3K27ac_Scrambled_DMSO

tag: strain background

tag: shRNA

value: Pu.1 Scrambled

tag: treatment

value: DMSO

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: KMMd21_rep2

city: Xuzhou

first: Hui

last: Liu

state: Jiangsu

address: #1 Daxue Road

institute: China University of Mining and Technology

data_processing:
Library strategy: CRISPR screen
CRISPR screen sequencing data processing was performed faithfully following the previously described protocol of Feng Zhang lab (Shalem et al., 2014).
After trimming of the adaptor sequences, the reads were mapped to the sgRNA library.
The summarized reads counting of each sgRNA for each sample is presented in the processed data file.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include reads count of each sgRNA for each CRISPR screening samples

organism: Rattus norvegicus

source_name: KMM cell

growth_protocol: Rat primary embryonic mesenchymal stem cells (MM), KSHV-transformed MM cells (KMM) were maintained in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS; Sigma-Aldrich), 4 mM L-glutamine, and 10 µg/ml penicillin and streptomycin.

extract_protocol:
Genomic DNA was extracted using QiAMP kit (Qiagen) and PCR was performed in two steps. First, the input genomic DNA was amplified by 30 cycles in order to achieve 300X coverage over the sgRNA library using the primers F1: TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TAT CTT GTG GAA AGG ACG AAA and R1: GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT ATT TTA ACT TGC TAT TTC TAG CTC. Then, to attach Illumina adaptors and barcode samples, a second PCR reaction was carried out by 6 cycles using 20ng purified PCR product and the primers F2: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, and R2:GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG.  Amplicons from the second PCR were gel-extracted, quantified, mixed and sequenced using HiSeq 2500 (Illumina).
Rat sgRNA library (Toolgen Rat genome RGEN library v1.0) was constructed by Toolgen (www.toolgen.com).
Amplified oligos in oligo library (Type:CTTGTGGAAAGGACGAAACACCG-X20-GTTTTAGAGCTAGAAATAGCAAGTTAAA) with ArrayF ( TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCG  ) and ArrayR (ACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC  ) were inserted into BsmB1-cut pLKO.1 Lentiviral plasmid.

treatment_protocol: We first generated MM and KMM cells stably expressing Cas9 by lentiviral transduction following by positive selection with blasticidin for 1 week. We then generated a library of sgRNAs targeting 19,840 genes of the rat genome, each with 3 independent sgRNAs. Cas9-expressing MM and KMM cells were transduced with the lentiviral sgRNA library via spinfection at a MOI of 0.3 and selected for 3 days with puromycin. The cultures were then switched to normal medium without any selection and cell samples were collected at day 1, 4, 11 and 21 after transduction, and subjected to DNA sequencing to determine the gain and loss sgRNAs over time.

tag: infection status

value: KSHV-infected

value: mesenchymal stem cell

tag: surviving days


title: H3K27ac_Pu-1_shRNA2_LSD1i

tag: cell line

value: Pu.1 shRNA2


title: b6_lcmv_cd8_nav_r2_RNAseq

source_name: BMC F1 Spleen B6 naïve CD8 T cell

tag: strain

value: Spleen

tag: cell type

value: Naive CD8 T cell


title: H3K27ac_Pu-1_shRNA2_DMSO

tag: tissue source


title: KMMd21_rep3


title: DLD1 siCONT plus TSA replicate2

description:
DLD1 with control siRNA plus TSA replicate2
DLD1-siCONT-TSA-2

source_name: DLD1 with control siRNA plus TSA

tag: sirna

value: control

tag: genotype

tag: agent

value: Trichostatin A


title: KMMd11_rep2

tag: tissue


title: DLD1 siCONT replicate1

description:
DLD1 with control siRNA plus mock replicate1
DLD1-siCONT-1

source_name: DLD1 with control siRNA plus mock

value: mock