title: 0422051G V2 wk 2

description: PAXgene Sample


title: 0650988L V1 wk 0

status: Public on Mar 18 2021

type: RNA

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

country: USA

institute: Case Western Reserve University

description: PAXgene Sample

hyb_protocol: Standard Illumina hybridization protocol for HumanHT-12_V4 BeadChips.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the neqc function with limma in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Blood

label_protocol: Biotinylated cRNA was oligo-dT primed and prepared with the Illumina TotalPrep RNA amplification kits (Ambion).

extract_protocol: Total RNA was extracted using Qiagen's PreAnalytix PAXgene Blood RNA kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Globin removal was conducted with ThermoFisher's GLOBINclear kit. Quality control was performed with Bio-Rad's Experion.

tag: hiv status

value: HIV Positive

tag: donor id

tag: timepoint

tag: timepoint unit

value: wk

tag: visit

tag: age in years


title: 0650018B BL day 0

description: PAXgene Sample

value: day

value: BL


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep2

type: SRA

city: Boston

first: Jingyi

last: Wu

state: MA

address: 360 Longwood Ave

department: Department of Cancer Biology

institute: Dana-Farber Cancer Institute

library_source: transcriptomic

data_processing:
cellranger (version 3.0.1) mkfastq was run on defaults to demultiplex bcl files. Cellranger counts was used to generate filtered_feature_matrix.h5
cellranger filtered_feature_matrix .h5
Genome_build: Grcm38
Base-calling was performed using bcl2fastq2-v2.20.0

molecule: polyA RNA

organism: Mus musculus

source_name: CD4/8+ enriched immune cells from Lewis lung carcinoma tumors - in vivo

growth_protocol: All cell lines were tested for mycoplasma and cultured in RPMI (VWR) or DMEM media (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
Following harvest of tumors, CD4+/CD8+ immune cells were enriched with positive selection using MACS beads/columns and isolated as single cells using droplet-based instrumentation (10x Chromium).
Single-cell RNA sequencing libraries were constructed with 10x chromium 5' reagents.

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to LLC cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). Cells were then inoculated into the flanks of recipient WT mice, expanded in vivo for 15 days (+/- PD-1/CTLA-4 blockade), and then harvested.

tag: cell type


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_pd1_ctla4_treatment_rep1

value: CD4/8+ enriched immune cells from Lewis lung carcinoma tumors - in vivo


title: 8501580G V2 wk 2

description: PAXgene Sample


title: LLC_Setdb1_PolyIC_experiment_2_rep2

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Setdb1_PolyIC_rep2_quant

data_processing:
Paired and unpaired reads were aligned using salmon  (version 0.14.1) with parameters --gcBias --seqBias --validateMappings. Summary to gene level quantification was performed using Tximport (version 1.14.2)
genome build: Genome Reference Consortium Mouse Build 38 release 93
gene-by-sample raw count matrix
Base-calling was performed using bcl2fastq2-v2.20.0

source_name: Lewis lung carcinoma  - in vitro

extract_protocol:
Approximately one million cells per sample were resuspended in RLT lysis buffer with ß-mercaptoethanol (1:100 dilution) and total RNA was isolated using an RNeasy Kit.
Poly(A)-enriched sequencing libraries were constructed with the NEBNext Ultra RNA Library Prep Kit (New England Biolabs).

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to B16 cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). No additional treatments were administered.

tag: genotype

value: Setdb1 KO


title: LLC_Setdb1_PolyIC_experiment_2_rep1

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Setdb1_PolyIC_rep1_quant


title: 0140353J BL day 0

description: PAXgene Sample


title: 0509463B BL day 0

description: PAXgene Sample


title: 0460965H V2 wk 2

description: PAXgene Sample


title: 0670642F V1 day 21

description: PAXgene Sample


title: 0509858G V2 wk 2

description: PAXgene Sample


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_no_treatment_rep4


title: scRNA-seq_gex_LLC_CD4-CD8pos_control_sg5_no_treatment_rep3


title: LLC_Setdb1_NoTx_experiment_2_rep1

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Setdb1_NoTx_rep1_quant


title: LLC_Setdb1_NoTx_experiment_2_rep2

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Setdb1_NoTx_rep2_quant


title: LLC_Ctrl_PolyIC_experiment_2_rep2

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Ctrl_PolyIC_rep2_quant

value: control


title: LLC_Ctrl_PolyIC_experiment_2_rep1

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Ctrl_PolyIC_rep1_quant


title: LLC_Ctrl_NoTx_experiment_2_rep1

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Ctrl_NoTx_rep1_quant


title: B16_Setdb1_PolyIC_experiment_2_rep2

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Setdb1_PolyIC_rep2_quant

source_name: B16 melanoma - in vitro


title: LLC_Ctrl_NoTx_experiment_2_rep2

description:
LLC_counts_GRCM38_experiment2.txt
LLC_Ctrl_Ctrl_NoTx_rep2_quant


title: 0650002D BL day 0

description: PAXgene Sample


title: 0660033H V1 wk 3

description: PAXgene Sample


title: B16_Setdb1_NoTx_experiment_2_rep1

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Setdb1_NoTx_rep1_quant


title: 0509858G BL wk 0

description: PAXgene Sample


title: B16_Setdb1_PolyIC_experiment_2_rep1

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Setdb1_PolyIC_rep1_quant


title: B16_Setdb1_NoTx_experiment_2_rep2

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Setdb1_NoTx_rep2_quant


title: B16_Ctrl_PolyIC_experiment_2_rep2

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Ctrl_PolyIC_rep2_quant


title: 0651098E V1 wk 0

description: PAXgene Sample


title: B16_Ctrl_PolyIC_experiment_2_rep1

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Ctrl_PolyIC_rep1_quant


title: B16_Ctrl_NoTx_experiment_2_rep1

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Ctrl_NoTx_rep1_quant


title: B16_Ctrl_NoTx_experiment_2_rep2

description:
B16_counts_GRCM38_experiment2.txt
B16_Ctrl_Ctrl_NoTx_rep2_quant


title: 0450398B BL wk 0

description: PAXgene Sample


title: 0651037A V2 wk 2

description: PAXgene Sample


title: 0504805L V1 wk 3

description: PAXgene Sample


title: 0380990L V1 wk 3

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_Tx_rep4

data_processing:
cellranger (version 3.0.1) mkfastq was run on defaults to demultiplex bcl files. Cellranger counts was used to generate filtered_feature_matrix.h5
genome build: Genome Reference Consortium Mouse Build 38 release 93
cellranger filtered_feature_matrix .h5
Base-calling was performed using bcl2fastq2-v2.20.0

source_name: CD45+-enriched immune cells from Lewis lung carcinoma tumors - in vivo

extract_protocol:
Following harvest of tumors, CD45+ immune cells were enriched with positive selection using MACS beads/columns and isolated as single cells using droplet-based instrumentation (10x Chromium).
Single-cell RNA sequencing libraries were constructed with 10x chromium 3' reagents.


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_UnTx_rep3

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to LLC cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). Cells were then inoculated into the flanks of recipient WT mice, expanded in vivo for 15 days without PD1/CTLA-4 treatment, and then harvested.


title: 0650018B V1 wk 0

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_UnTx_rep2


title: 8502564L BL day 0

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_UnTx_rep1


title: 0670198K V1 wk 3

description: PAXgene Sample


title: 8502633B V1 wk 3

description: PAXgene Sample


title: 0730095D V1 day 21

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_Tx_rep3


title: 8501932K V1 wk 3

description: PAXgene Sample


title: 0506178K BL day 0

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_Tx_rep1


title: 0650002D V1 wk 0

description: PAXgene Sample


title: 0670642F BL day 0

description: PAXgene Sample


title: 8502572C V1 wk 4

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_UnTx_rep3


title: 8502634L BL wk 0

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_UnTx_rep2


title: scRNA-seq_LLC_CD45pos_llc_setdb1_sg4_Tx_rep2


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_UnTx_rep1


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_Tx_rep4


title: 8502634L V2 wk 2

description: PAXgene Sample


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_Tx_rep1


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_Tx_rep3


title: scRNA-seq_LLC_CD45pos_llc_control_sg5_Tx_rep2


title: RNA-seq_LLC_control_sg5_UnTx_rep_10

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep10

data_processing:
RNA-seq reads were trimmed using trimmomatic (version 0.36) with the following settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:130. Paired and unpaired reads were aligned using salmon  (version 0.14.1) with parameters --gcBias --seqBias --validateMappings. Summary to gene level quantification was performed using Tximport (version 1.14.2)
genome build: Genome Reference Consortium Mouse Build 38 release 93
gene-by-sample raw count matrix
Base-calling was performed using bcl2fastq2-v2.20.0

source_name: Lewis lung carcinoma tumors  - in vivo

extract_protocol:
Approximately 40mg of tumor tissue per sample was submerged in RNAlater reagent, frozen, and homogenized via a TissueLyser II instrument.
Poly(A)-enriched sequencing libraries were constructed with the NEBNext Ultra RNA Library Prep Kit (New England Biolabs).


title: RNA-seq_LLC_control_sg5_UnTx_rep_8

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep8


title: RNA-seq_LLC_control_sg5_UnTx_rep_7

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep7


title: 0670198K BL wk 0

description: PAXgene Sample


title: 0503339L V2 wk 2

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_UnTx_rep_6

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep6


title: RNA-seq_LLC_control_sg5_UnTx_rep_5

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep5


title: RNA-seq_LLC_control_sg5_UnTx_rep_2

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep2


title: RNA-seq_LLC_control_sg5_UnTx_rep_3

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep3


title: 0422274G V1 wk 3

description: PAXgene Sample


title: 0509463B V1 wk 3

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_UnTx_rep_9

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep9


title: 0362634F V1 wk 3

description: PAXgene Sample


title: 0460965H V1 wk 0

description: PAXgene Sample


title: 0660033H BL day 0

description: PAXgene Sample


title: 8500063B V1 wk 3

description: PAXgene Sample


title: 0362634F BL day 0

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_Tx_rep_6

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_Tx_rep6


title: 0730028D V1 day 21

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_UnTx_rep_1

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep1


title: 0290127H V2 wk 2

description: PAXgene Sample


title: 0730166B BL day 0

description: PAXgene Sample


title: 8501580G V1 wk 3

description: PAXgene Sample


title: 0111069G V2 day 10

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_Tx_rep_4

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_Tx_rep4


title: 0460965H BL wk 0

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_Tx_rep_3

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_Tx_rep3


title: 8502572C BL day 0

description: PAXgene Sample


title: 0730028D BL day 0

description: PAXgene Sample


title: 0400354A BL day 0

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_Tx_rep_2

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_Tx_rep2


title: 0503302F V1 day 21

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_Tx_rep_1

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_Tx_rep1


title: 0505135K V1 wk 0

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_10

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep10


title: RNA-seq_LLC_control_sg5_Tx_rep_5

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_Tx_rep5


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_9

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep9


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_7

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep7


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_8

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep8


title: 8500403L V1 wk 3

description: PAXgene Sample


title: 8502745G BL day 0

description: PAXgene Sample


title: 0370215C BL day 0

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_6

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep6


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_3

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep3


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_5

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep5


title: 0290127H BL wk 0

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_1

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep1


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_4

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep4


title: 0450007G BL wk 0

description: PAXgene Sample


title: 8502633B BL wk 0

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_7

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep7

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to LLC cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). Cells were then inoculated into the flanks of recipient WT mice, expanded in vivo for 15 days, treated with 200 µg PD1/CTLA-4 on Days 6, 9, 12, and then harvested.


title: 0504866C V2 wk 2

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_6

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep6


title: 8501580G BL day 0

description: PAXgene Sample


title: 0361442C V1 wk 3

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_5

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep5


title: 0506497E BL day 0

description: PAXgene Sample


title: 8502062B V1 wk 3

description: PAXgene Sample


title: 8501845F V1 day 21

description: PAXgene Sample


title: 0509277H V1 day 21

description: PAXgene Sample


title: 0422274G BL day 0

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_4

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep4


title: RNA-seq_LLC_setdb1_sg4_UnTx_rep_2

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_UnTx_rep2


title: 0509638A V1 wk 3

description: PAXgene Sample


title: 0111352E V2 wk 2

description: PAXgene Sample


title: 0360047A V2 wk 5

description: PAXgene Sample


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_2

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep2


title: RNA-seq_B16_KO_sg2_rep2

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt

data_processing:
RNA-seq reads were aligned to the mm9 genomes by HISAT2 with default parameters. All unmapped reads were removed. Read counts were calculated by featureCounts using uniquely mapped reads, and differentially expressed genes were identified by DESeq2 with a cutoff of more than 1.5 fold-change and a p-value of less than 0.05. The gene expression level (FPKM) was calculated by StringTie based on the mm9 refFlat annotation database. To quantify the expression of TEs, RPKM values were calculated based on the mm9 RepeatMasker annotations using uniquely mapped RNA-seq reads.
genome build: mm9
normalized abundance measurements
Base-calling was performed using bcl2fastq2-v2.20.0

extract_protocol:
Approximately one million cells per sample were resuspended in RLT lysis buffer with ß-mercaptoethanol (1:100 dilution) and total RNA was isolated using an RNeasy Kit.
Poly(A)-enriched sequencing libraries were constructed with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_1

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep1


title: RNA-seq_LLC_setdb1_sg4_Tx_rep_3

description:
Invivo_LLC_counts_GRCm38.txt
llc_setdb1_sg4_Tx_rep3


title: RNA-seq_B16_KO_sg2_rep1

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: RNA-seq_B16_KO_sg1_rep2

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: 0504806I V1 wk 3

description: PAXgene Sample


title: RNA-seq_B16_control_sg2_rep1

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: RNA-seq_B16_control_sg2_rep2

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: RNA-seq_B16_control_sg1_rep2

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: RNA-seq_B16_KO_sg1_rep1

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: 0509463B V2 wk 2

description: PAXgene Sample


title: RNA-seq_B16_control_sg1_rep1

description:
B16_FPKM_mm9.txt
B16_counts_mm9.txt


title: RNA-seq_LLC_KO_sg2_rep2

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt

treatment_protocol: CRISPR knock-out (KO) was performed via delivery of CAS9 and sgRNA to LLC cells.  When indicated, cells were selected using standard agents (blasticidin, puromycin, hygromycin). No additional treatments were administered.


title: RNA-seq_LLC_KO_sg1_rep2

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: 8502745G V2 wk 2

description: PAXgene Sample


title: RNA-seq_LLC_KO_sg1_rep1

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: RNA-seq_LLC_KO_sg2_rep1

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: 0651037A BL day 0

description: PAXgene Sample


title: 0111352E BL wk 0

description: PAXgene Sample


title: RNA-seq_LLC_control_sg5_UnTx_rep_4

description:
Invivo_LLC_counts_GRCm38.txt
llc_control_sg5_UnTx_rep4


title: 0509277H V2 wk 2

description: PAXgene Sample


title: 0650002D V2 day 10

description: PAXgene Sample


title: 0504806I BL wk 0

description: PAXgene Sample


title: 0422273I BL day 0

description: PAXgene Sample


title: 0690745F V1 wk 0

description: PAXgene Sample


title: 0360675B V1 wk 3

description: PAXgene Sample


title: RNA-seq_LLC_control_sg2_rep2

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: 0509638A BL day 0

description: PAXgene Sample


title: 0651098E BL wk 0

description: PAXgene Sample


title: 0504169L V1 wk 3

description: PAXgene Sample


title: RNA-seq_LLC_control_sg1_rep2

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: 0140353J V2 wk 2

description: PAXgene Sample


title: RNA-seq_LLC_control_sg2_rep1

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: 8501932K V2 wk 2

description: PAXgene Sample


title: 0470244A V2 wk 2

description: PAXgene Sample


title: 0360675B V2 wk 2

description: PAXgene Sample


title: 0470090H BL day 0

description: PAXgene Sample


title: ATAC-seq_B16_KO_sg2_rep1

library_source: genomic

data_processing:
ATAC-seq reads were first trimmed by Trim Galore (v0.4.5) to remove adapter sequences. The trimmed reads were aligned to mm9 by Bowtie(v2.2.2) with the parameters: -N 1 -L 25 -X 2000 –no-mixed –no-discordant.All unmapped reads and PCR duplicates were removed. Non-uniquely mapped reads were assigned to the position with the best matched score. All ATAC sites were called by the MACS2(v2.1.1) callpeak function with the parameters –nolambda –nomodel.
genome build: mm9
WIG
Base-calling was performed using bcl2fastq2-v2.20.0

molecule: genomic DNA

extract_protocol:
Nuclei from 50,000 cells per sample were isolated with Nuclei EZ buffer.
Isolated nuclei were subjected to tagmentation with Tn5 transposase and library construction with the Nextera DNA Library Prep Kit (Illumina)


title: ATAC-seq_B16_KO_sg1_rep2


title: ATAC-seq_B16_KO_sg1_rep1


title: ATAC-seq_B16_control_sg2_rep1


title: ATAC-seq_B16_control_sg1_rep1


title: ATAC-seq_B16_control_sg1_rep2


title: 0111069G BL day 0

description: PAXgene Sample


title: ATAC-seq_B16_control_sg2_rep2


title: 8500403L V2 wk 2

description: PAXgene Sample


title: 0503218F V2 wk 2

description: PAXgene Sample


title: 0381130J V1 wk 3

description: PAXgene Sample


title: 0361047L V1 wk 3

description: PAXgene Sample


title: 0505382H V2 day 10

description: PAXgene Sample


title: 0730095D V2 wk 2

description: PAXgene Sample


title: 0381134B V2 wk 2

description: PAXgene Sample


title: 0110629K V1 day 21

description: PAXgene Sample


title: ATAC-seq_LLC_KO_sg1_rep1

source_name: Lewis lung carcinoma - in vitro


title: Ncclr-4_4h_1

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

country: China

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 or Neurospora crassa FGSC 2489 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html) and Neurospora crassa OR74A genome (version 12)
Supplementary_files_format_and_content: tab-delimited text files including Reads count for each sample.

organism: Neurospora crassa

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation. N. crassa strains were inoculated into 1×Vogel’s salt with 2% sucrose and grown for 16 h at 25 °C. Mycelia of the N. crassa were collected and washed with 1×Vogel’s salt several times, and transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: FGSC 2489

tag: genotype/variation


title: Ncclr-4_4h_2


title: ATAC-seq_LLC_KO_sg2_rep1


title: ATAC-seq_LLC_control_sg1_rep1


title: 0110629K V2 wk 2

description: PAXgene Sample


title: 0470244A BL day 0

description: PAXgene Sample


title: hiPSC-derive neural progenitor cells

city: La Jolla

first: Dorit

last: Trudler

state: CA

address: 11119 N Torrey Pines Rd. Suite 125

institute: The Scripps Research Institute

data_processing:
Data quality was assessed using FastQC (version 0.10.1) before being mapped to known Ensemble genes (GRCh37/NCBIM37) using Tophat2 (version 2.0.13).
Raw read counts for each gene were obtained using Subread (version 1.4.2).
Raw read counts were normalized using the trimmed mean of M-values (TMM) method (M. D. Robinson, A. Oshlack, Genome Biol., 2010), and precision weights were calculated using voom (C. W. Law, Genome Biol., 2014) prior to differential analysis using the limma empirical Bayes analysis pipeline (G. K. Smyth, at. Appl. Genet. Mol. Biol., 2004).
Genome_build: GRCh37/NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include raw read counts

growth_protocol: All cells were cultured at 37°C in 5% CO2 and grown in their appropriate media.

extract_protocol:
Cells were removed and collected on ice and RNA was harvested using Quick-RNA™ MiniPrep kit (Zymo Research, # R1055).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neural progenitor cells


title: RNA-seq_LLC_control_sg1_rep1

description:
LLC_FPKM_mm9.txt
LLC_counts_mm9.txt


title: 0450007G V2 wk 2

description: PAXgene Sample


title: human fetal microglia rep 2

source_name: fetal microglia (Clonexpress, #HMG030)

value: microglia


title: 0503923A V2 wk 2

description: PAXgene Sample


title: 0111069G V1 wk 3

description: PAXgene Sample


title: 0380990L BL wk 0

description: PAXgene Sample


title: 0370121L V2 wk 2

description: PAXgene Sample


title: 0503302F BL wk 0

description: PAXgene Sample


title: 0450398B V2 wk 2

description: PAXgene Sample


title: 0411308F V2 wk 2

description: PAXgene Sample


title: H3K27ac_ChIP-seq_B16_KO_sg1_rep2

data_processing:
Library strategy: MINT_ChIP-seq
ChIP-seq reads were first trimmed by Trim Galore (v0.4.5) to remove adapter sequences. The trimmed reads were aligned to mm9 by Bowtie (v2.2.2) with the parameters –N 1 –L 25 -X 2000 --no-mixed --no-discordant. All unmapped reads and PCR duplicates were removed. Non-uniquely mapped reads were assigned to the position with the best matched score. For downstream analyses, we normalized read counts by computing the numbers of reads per kilobase of bin per million of reads (RPKM).
genome build: mm9
WIG
Base-calling was performed using bcl2fastq2-v2.20.0

extract_protocol:
250,000 cells per sample were fragmented with micrococcal nuclease (MNase)-based fragmentation and immunoprecipitation was performed with anti-H3K27ac (Active Motif, 39133) antibody.
Sequencing libraries were constructed via in vitro transcription of adapter ligated DNA followed by reverse transcription/cDNA synthesis and a final library PCR to enrich adapter-modified DNA fragments.

tag: antibody


title: H3K27ac_ChIP-seq_B16_KO_sg1_rep1


title: human fetal microglia rep 1


title: H3K27ac_ChIP-seq_B16_KO_sg2_rep1


title: H3K27ac_ChIP-seq_B16_KO_sg2_rep2


title: ATAC-seq_B16_KO_sg2_rep2


title: hiPSC rep 2

value: induced pluripotent stem cells


title: 0381378I BL wk 3

description: PAXgene Sample


title: H3K27ac_ChIP-seq_B16_control_sg2_rep2


title: hiPSC-derived microglia rep2


title: hiPSC-derived microglia rep1


title: hiPSC rep 1


title: H3K27ac_ChIP-seq_B16_control_sg1_rep1

extract_protocol:
250,000 cells per sample were fragmented with micrococcal nuclease (MNase) and subjected to T7 adapter ligation and pooling prior to immunoprecipitation with anti-H3K27ac (Active Motif, 39133) antibody and magnetic protein G dynabeads.
Sequencing libraries were constructed via in vitro transcription of adapter ligated DNA followed by reverse transcription/cDNA synthesis and a final library PCR to enrich adapter-modified DNA fragments.


title: H3K27ac_ChIP-seq_B16_control_sg1_rep2


title: 0381130J V2 wk 2

description: PAXgene Sample


title: H3K9me3_ChIP-seq_B16_KO_rep2

data_processing:
ChIP-seq reads  were first trimmed by Trim Galore (v0.4.5) to remove adapter sequences. The trimmed reads were aligned to mm9 by Bowtie (v2.2.2) with the parameters –N 1 –L 25 -X 2000 --no-mixed --no-discordant. All unmapped reads and PCR duplicates were removed. Non-uniquely mapped reads were assigned to the position with the best matched score. For downstream analyses, we normalized read counts by computing the numbers of reads per kilobase of bin per million of reads (RPKM). H3K9me3 peaks were identified by calculating RPKM in the 100bp bin first. According to the signal distribution, each bin with RPKM more than 0.15 was selected as the signal bin. Signal bins within 500bp of each other were merged and called as signals/peaks.
genome build: mm9
WIG
Base-calling was performed using bcl2fastq2-v2.20.0

extract_protocol:
Ten million cells per sample were cross-linked with 1% formaldehyde for 15 min, quenched with glycine, and subjected to two-step cell and nuclear lysis in the presence of protease inhibitors. Shearing of samples were optimized such that the final DNA length was approximately 400 base pairs using a Branson sonifier, and was followed by immunoprecipitation with anti-H3K9me3 polyclonal antibody (Abcam, ab8898) and 50:50 mixes of magnetic Protein A and G dynabeads (Invitrogen).
End-repair, A-tailing, adapter ligation, and library amplification were performed with the Kapa HyperPrep kit (Roche).


title: H3K9me3_ChIP-seq_B16_KO_rep1

extract_protocol:
Ten million cells per sample were cross-linked with 1% formaldehyde for 15 min, quenched with glycine, and subjected to two-step cell and nuclear lysis in the presence of protease inhibitors. Shearing of samples were optimized such that the final DNA length was approximately 400 base pairs using a Branson sonifier, and was followed by incubation with anti-H3K9me3 polyclonal antibody (Abcam, ab8898) overnight at 4˚C. Immunoprecipitation was performed with 50:50 mixes of magnetic dynabeads Protein A and G (Invitrogen).
End-repair, A-tailing, adapter ligation, and library amplification were performed with the Kapa HyperPrep kit (Roche).


title: 0500079E BL wk 0

description: PAXgene Sample


title: 8501364E V1 day 0

description: PAXgene Sample


title: 0470090H V1 wk 3

description: PAXgene Sample


title: H3K9me3_ChIP-seq_B16_control_rep2


title: 0506178K V1 day 0

description: PAXgene Sample


title: H3K27ac_ChIP-seq_B16_control_sg2_rep1


title: 8501845F BL wk 0

description: PAXgene Sample


title: 0504866C BL wk 0

description: PAXgene Sample


title: 0361196G V2 wk 2

description: PAXgene Sample


title: 8502062B V2 wk 2

description: PAXgene Sample


title: 8502564L V2 day 10

description: PAXgene Sample


title: 8502633B V2 wk 2

description: PAXgene Sample


title: 0506497E V2 day 10

description: PAXgene Sample


title: 0360047A BL day 0

description: PAXgene Sample


title: 0650018B V2 wk 2

description: PAXgene Sample


title: H3K9me3_ChIP-seq_B16_control_rep1


title: 0509638A V2 day 10

description: PAXgene Sample


title: 0670198K V2 wk 2

description: PAXgene Sample


title: 0361047L V2 wk 2

description: PAXgene Sample


title: H3K9me3_ChIP-seq_LLC_KO_rep2


title: 0690972E V2 wk 2

description: PAXgene Sample


title: 0690745F V2 wk 2

description: PAXgene Sample


title: 0509858G V1 wk 3

description: PAXgene Sample


title: 0670642F V2 day 10

description: PAXgene Sample


title: H3K9me3_ChIP-seq_LLC_KO_rep1


title: H3K9me3_ChIP-seq_LLC_control_rep2


title: H3K9me3_ChIP-seq_LLC_control_rep1


title: Tumor_Bicc1_intra_rep3

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

description: cholangiocarcinoma derived by transplantation of Tp53 null C57BL/6 organoids expressing FGFR2-BICC1

data_processing:
Base-calling was performed by Illumina Real-Time Analysis (RTA) software and NextSeq Control Software (NCS).
Raw reads were aligned using STAR (Dobin et al., 2013) version 2.5.3a to build version mm10 of the mouse genome.
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package (Liao et al., 2014).
Normalization was carried out using edgeR R package (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix of raw counts for each sample

source_name: Cholangiocarcinoma

growth_protocol: s.c. tumors were excised when volume reached 300-500 mm3. Liver tumors were obtained upon euthanasy of moribund mice

extract_protocol:
Total RNA was extracted with QIAzol andpurified with the miRNeasyMini kit (Qiagen). RNA was quantified using the Qubit® RNA HS Assay Kit (Thermo Fischer Scientific). RNA integrity (RIN) was measured using the Bioanalyzer 2100 RNA 6000 Nano Kit (Agilent Technologies). High-quality total RNA was assessed for all samples, with RIN values ranging from 8.0 to 10.0.
TruSeq® Stranded mRNA Kit (Illumina) was used to generate all libraries, according to the manufacturer's recommendations. Produced libraries were quantified by Qubit® DNA HS Assay Kit (Thermo Fischer Scientific) and Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).
RNA-seq. An equimolar libraries pool (14 samples) was loaded onto Illumina NextSeq 500 platform into a High Output Kit v2.5 cartridge (2x75 bp paired-end sequencing with about 25 million clusters per sample).

value: NOD SCID

tag: tumor localization

value: intra-hepatic

tag: fusion


title: Tumor_Bicc1_intra_rep2


title: 0370215C V2 wk 2

description: PAXgene Sample


title: ATAC-seq_LLC_control_sg2_rep1


title: Tumor_Bicc1_sc_rep2

description: s.c. cholangiocarcinoma derived by transplantation of Tp53 null C57BL/6 organoids expressing FGFR2-BICC1

value: sub cutaneous


title: Tumor_Bicc1_sc_rep1


title: 8500171C V2 day 10

description: PAXgene Sample


title: 0400354A V1 day 21

description: PAXgene Sample


title: 0422273I V1 wk 3

description: PAXgene Sample


title: 0503923A BL day 0

description: PAXgene Sample


title: 0400444L V2 wk 2

description: PAXgene Sample


title: 0411308F BL day 0

description: PAXgene Sample


title: 8502062B BL day 0

description: PAXgene Sample


title: 0505135K V2 day 10

description: PAXgene Sample


title: 0422273I V2 wk 1

description: PAXgene Sample


title: 0422051G V1 wk 3

description: PAXgene Sample


title: 0140360C BL day 0

description: PAXgene Sample


title: 0400354A V2 day 10

description: PAXgene Sample


title: 8500171C V1 day 0

description: PAXgene Sample


title: Tumor_Tacc3_sc_2Gen_rep2

description: s.c. cholangiocarcinoma derived by transplantation of Tp53 null C57BL/6 tumoroids expressing FGFR2-TACC3


title: 8502745G V1 wk 3

description: PAXgene Sample


title: 0370215C V1 wk 3

description: PAXgene Sample


title: HepaRG_cell_triclosan_0.050mM_bile_acid_mix_2

city: Jette

first: Eva

middle: Anne D

last: Gijbels

state: Brussels

address: Laarbeeklaan 103, Building G, 2th floor, Department IVTD

country: Belgium

institute: VUB

description: Gene expression of human hepatoma HepaRG cells after 72 hours treatment with 0.050 mM triclosan and the 50 x concentrated bile acid mixture

hyb_protocol: 12.5 μg of fragmented amplified RNA was hybridized to Affymetrix Human genome U133 plus 2.0 GeneChip. Subsequently, the chips were placed in a GeneChip Hybridization Oven 645 (Affymetrix, Germany). After incubation, the arrays were washed with GeneChip Fluidics Station 450 (Affymetrix, Germany) and stained with Affymetrix HWS kit.

scan_protocol: Stained arrays were scanned via an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Robust Multichip Average (RMA) Express was utilized for normalization and summarization.
Background adjustment, quantile normalization and summarization using median polish was executed via RMA Expression Software.

label: Biotin

source_name: Cell lysates of HepaRG cells treated with 0.050 mM triclosan and the 50 x concentrated bile acid mix

label_protocol: 100 ng total RNA per sample was amplified using a GeneChip 3′IVT Express Kit following manufacturer’s instructions (Affymetrix, Germany). Amplified RNA was purified with magnetic beads and 15 mg biotin-amplified RNA was treated with fragmentation reagent.

growth_protocol: Cryopreserved differentiated HepaRG cells (Biopredic International, France) were thawed and seeded following manufacturer’s instructions with basal hepatic cell medium (Williams’ E basal medium with GlutaMAX containing phenol red, Biopredic International, France) supplemented with thaw seed and general purpose medium (Biopredic International, France). Hereafter, HepaRG cells were maintained in basal hepatic cell medium supplemented with maintenance and metabolism medium (Biopredic International, France) and refreshed every 2–3 days. Cells were treated from day 7 after seeding.

extract_protocol: Total RNA was extracted using the Rneasy mini kit (Qiagen, Belgium)

treatment_protocol: HepaRG cells were treated with acetaminophen, sunset yellow, tartrazine and triclosan in the  presence of a 50 x concentrated bile acid mixture.

tag: cell line

value: HepaRG cells

tag: treatment

value: TRI + BA


title: HepaRG_cell_triclosan_0.050mM_bile_acid_mix_1


title: 0361047L BL day 0

description: PAXgene Sample


title: HepaRG_cell_triclosan_0.050mM_bile_acid_mix_3


title: Tumor_Bicc1_intra_rep1

value: NOD SCiID


title: 0503218F V1 wk 3

description: PAXgene Sample

value: HIV Positive


title: 0450007G V1 wk 3

description: PAXgene Sample

value: wk


title: 0411308F V1 wk 3

description: PAXgene Sample


title: Tumor_Tacc3_sc_2Gen_rep1


title: Tumor_Tacc3_intra_rep3

description: cholangiocarcinoma derived by transplantation of Tp53 null C57BL/6 liver organoids expressing FGFR2-TACC3


title: Tumor_Tacc3_sc_rep1

description: s.c. cholangiocarcinoma derived by transplantation of Tp53 null C57BL/6 liver organoids expressing FGFR2-TACC3

value: NOD-SCID


title: 8500403L BL day 0

description: PAXgene Sample

value: day

value: BL


title: Tumor_Tacc3_intra_rep2

description: Cholangiocarcinoma derived by transplantation of Tp53 null C57BL/6 liver organoids expressing FGFR2-TACC3


title: Tumor_Tacc3_sc_rep2


title: Tumor_Tacc3_intra_rep1


title: HepaRG_cell_tartrazine_50mM_bile_acid_mix_3

description: Gene expression of human hepatoma HepaRG cells after 72 hours treatment with 50 mM tartrazine and the 50 x concentrated bile acid mixture

source_name: Cell lysates of HepaRG cells treated with 50 mM tartrazine and the 50 x concentrated bile acid mix

value: TART + BA


title: 0280750I BL day 0

description: PAXgene Sample


title: 0503218F BL day 0

description: PAXgene Sample


title: HepaRG_cell_sunset_yellow_10mM_bile_acid_mix_2

description: Gene expression of human hepatoma HepaRG cells after 72 hours treatment with 10 mM sunset yellow and the 50 x concentrated bile acid mixture

source_name: Cell lysates of HepaRG cells treated with 10 mM sunset yellow and the 50 x concentrated bile acid mix

value: SUN + BA


title: 0504169L BL day 0

description: PAXgene Sample


title: HepaRG_cell_sunset_yellow_10mM_bile_acid_mix_1


title: Liver_p53_homo

description: Liver from Tp53-/- C57BL/6 mice

source_name: Liver


title: HepaRG_cell_sunset_yellow_10mM_bile_acid_mix_3


title: 0503291A V2 wk 2

description: PAXgene Sample


title: HepaRG_cell_tartrazine_50mM_bile_acid_mix_2


title: 0400049I BL day 0

description: PAXgene Sample


title: 0503339L BL wk 0

description: PAXgene Sample


title: HepaRG_cell_tartrazine_50mM_bile_acid_mix_1


title: 8500171C BL day 0

description: PAXgene Sample


title: 0400049I V2 day 10

description: PAXgene Sample


title: 0400444L V1 wk 0

description: PAXgene Sample


title: 0380990L V2 wk 2

description: PAXgene Sample


title: 0361196G BL day 0

description: PAXgene Sample


title: 0140360C V1 wk 3

description: PAXgene Sample


title: Liver_p53_het

description: Liver from Tp53-/+ C57BL/6 mice


title: 0381134B BL wk 0

description: PAXgene Sample


title: 0422274G V2 wk 2

description: PAXgene Sample


title: 0290127H V1 wk 3

description: PAXgene Sample


title: 0690972E V1 wk 3

description: PAXgene Sample


title: 0362634F V2 wk 5

description: PAXgene Sample


title: HepaRG_cell_acetaminophen_13mM_bile_acid_mix_2

description: Gene expression of human hepatoma HepaRG cells after 72 hours treatment with 13 mM acetaminophen and the 50 x concentrated bile acid mixture

source_name: Cell lysates of HepaRG cells treated with 13 mM acetaminophen and the 50 x concentrated bile acid mix

value: APAP + BA


title: 0140360C V2 wk 3

description: PAXgene Sample


title: HepaRG_cell_acetaminophen_13mM_bile_acid_mix_1


title: HepaRG_cell_50x_bile_acid_mix_3

description: Gene expression of human hepatoma HepaRG cells after 72 hours treatment with the 50 x concentrated bile acid mixture

source_name: Cell lysates of HepaRG cells treated with the 50 x concentrated bile acid mix

value: BA


title: 0381378I V1 wk 3

description: PAXgene Sample


title: GLUT1KO.6

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.14, trimming for TrueSeq and polyA sequences. Reads were aligned to mouse genome build mm10 using HISAT2, v2.10 aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR TMM method.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID

source_name: Mouse lung tumour

growth_protocol: Tumors were initiated upon intratracheal instillation of 107 PFU per mouse of a commercially available adenoviral CMV-Flp vectors (Ad-CMV-Flp, Iowa University) to activate oncogenic KrasG12D and delete Tp53.

extract_protocol:
RNA from the CD45 negative fractions was extracted using TRIzol (15596018, ThermoFisher Scientific). TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500 ng total RNA.
We performed a TruSeq stranded mRNA LT prep, starting from 375 ng of RNA, according to Illumina protocol 15031047 Rev. E (internal exp code LPX170).

tag: gender

value: female

tag: tissue

value: Lung tumour

value: homozygous fl/fl

tag: group


title: HepaRG_cell_vehicle control_2

description: Gene expression of human hepatoma HepaRG cells after 72 hours treatment with the vehicle control

source_name: Cell lysates of HepaRG cells treated with the vehicle control

value: CTL


title: HepaRG_cell_50x_bile_acid_mix_1


title: 0504805L BL day 0

description: PAXgene Sample

source_name: Blood

tag: hiv status

tag: donor id


title: BL6_EF_1: adult NCSs (BL6) in EGF/FGF2 replica 1

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

country: United Kingdom

institute: University of Edinburgh

data_processing:
Single end RNA sequencing reads were trimmed with Trimgalore (version 0.5.0) with default parameters and aligned to mm10 genome using Kallisto (version 0.44.0).
Read counts were summarised via the package Tximport (version 1.8.0) and subsequent normalisation was completed via DESeq2 (version 1.27.32) as regularised-logarithm transformation (rlog).
Genome_build: mm10
Supplementary_files_format_and_content: Two sets of tab-delimited files for mouse NSCs containing raw counts, and normalised counts as calculated by DESeq2 (rlog).

source_name: Mouse Neural Stem Cell

growth_protocol: NSCs were isolated from the young adult 6-8 weeks old SVZ and maintained in vitro in serum-free basal medium supplemented with N2 and B27 (Life Technologies), Laminin-1 (Sigma, 1 μg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml each) (Bulstrode et al., 2016)

extract_protocol: RNA extraction was performed using the Qiagen RNeasy Plus minispin column kit, eluting in 50 µL of RNase-free water, and using an additional DNase step. RNA concentration was determined using the Qubit RNA High-Sensitivity kit (Life Technologies). Sample concentration and quality was assessed using the Aligent Tapestation and Nanodrop, only samples with a RIN value of 9.6 or above were used. For RNAseq we used RNA-Seq Quantification Library (Low input Library) BGISEQ-500RS.

treatment_protocol: Treatments with BMP-4 and FGF2/ BMP-4 were for 3 days. BMP-4 (10ng/ml, Peprotech, AF-120-05ET-100), FGF2 (10 ng/ml, Peprotech, # 100-18b, EGF (10ng/ml, Peprotech, #315-09)

value: Mouse Neural Stem Cell

tag: type


title: 0730166B V1 day 21

description: PAXgene Sample

extract_protocol: Total RNA was extracted using Qiagen's PreAnalytix PAXgene Blood RNA kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Globin removal was conducted with ThermoFisher's GLOBINclear kit. Quality control was performed with Bio-Rad's Experion.

tag: timepoint

tag: timepoint unit

tag: visit


title: BL6_EF_2: adult NCSs (BL6) in EGF/FGF2 replica 2

tag: cell type


title: 0500079E V2 day 3

description: PAXgene Sample

tag: age in years


title: HepaRG_cell_50x_bile_acid_mix_2

value: HepaRG cells


title: AD2_9_old

city: Novato

first: Tal

last: Ronnen Oron

address: 8001 Redwood blvd.

department: Bioinformatics Core

institute: Buck Institute for Research on Aging

data_processing:
remove short and low quality reads: Trimmomatic.  Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence.Data. Bioinformatics, btu170.
remove mitochondria originated reads: bowtie2, SAMtools 1.7. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-359. Published 2012 Mar 4. doi:10.1038/nmeth.1923; [4] Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup. The  Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352
remove reads mapped to black listed regions: BEDTools' intersect utility. https://github.com/Boyle-Lab/Blacklist/tree/master/lists
merge alignments from samples of the same experimental condition: SAMtools' merge utility. Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352
genomic coverage: deepTools bamcoverage utility. Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. “deepTools2: a next generation web server for deep-sequencing data analysis.” Nucleic Acids Research (2016): gkw257
Identify open genomic areas: ENCODE recommended pipeline, developed by Anshul Kundaje's lab at Stanford University. https://github.com/ENCODE-DCC/atac-seq-pipeline
Genome_build: dm6: Full genome sequences and annotations for Drosophila melanogaster (Fly) as provided by UCSC (dm6, Aug. 2014) http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Drosophila_melanogaster/UCSC/dm6/Drosophila_melanogaster_UCSC_dm6.tar.gz

organism: Drosophila melanogaster

source_name: intestinal stem cells

growth_protocol: Flies were raised and maintained on a standard yeast/molasses diet and kept at 25°C with 65% humidity on a 12 hour light/dark cycle.

extract_protocol:
Midguts of ~100-140 flies were dissected and dissociated using 0.5% Trypsin-EDTA and 100,000 YFP-labeled intestinal stem cells were isolated using FACS. Cells were collected into PBS and immediately spun down at 4°C, washed and lysed to release nuclei, which were then transposed using the Nextera DNA Sample prep kit (Illumina) according to manufacturer's instructions.
Transposed DNA was purified using MiniElute Reaction Cleaup kit (Qiagen). Transposed DNA was amplified using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs). Libraries were quantified by qPCR to determine the cycle number at which each sample produced 25% of maximum fluorescent intensity. The fluorescent intensity was used to estimate the number of additional PCR cycles required for each sample.

treatment_protocol: Flies were aged to indicated time-points (young, middle-aged and old), at which point they were dissected and intestinal stem cells were isolated.

value: intestine

tag: developmental stage

value: Old adult (60-65 days old)

tag: genotype

value: W Dah ; esg-Gal4, UAS-2xEYFP; Su(H)GBE-Gal80


title: 0470366D V2 wk 2

description: PAXgene Sample

value: HIV Positive

value: wk


title: HepaRG_cell_vehicle control_3


title: 0503339L V1 wk 3

description: PAXgene Sample


title: 0503923A V1 wk 3

description: PAXgene Sample


title: GLUT1KO.4

tag: strain


title: 8501809A BL day 0

description: PAXgene Sample

value: day


title: HepaRG_cell_vehicle control_1


title: BL6_BF_1: adult NCSs (BL6) treated with BMP4+FGF2 replica 1


title: GLUT1KO.5


title: BL6_BF_2: adult NCSs (BL6) treated with BMP4+FGF2 replica 2


title: BL6_B_2: adult NCSs (BL6) treated with BMP4 replica 2


title: GLUT1KO.3

value: male


title: 0280750I V1 wk 3

description: PAXgene Sample


title: GLUT1KO.2


title: AD2_6_mid

value: Middle-aged adult (29-31 days old)


title: AD2_8_old


title: GLUT1KO.1


title: BL6_B_1: adult NCSs (BL6) treated with BMP4 replica 1


title: 0503302F V2 wk 4

description: PAXgene Sample


title: AD2_3_mid


title: AD2_7_old


title: CTRL.6

value: homozygous wt/wt

value: control


title: AD2_2_young

value: Young adult (6-8 days old)


title: AD2_5_young


title: 0500079E V1 wk 0

description: PAXgene Sample


title: A4_EF_2: adult NCSs (ANS4) in EGF/FGF2 replica 2

value: ANS4 (A4)


title: A4_BF_2: adult NCSs (ANS4) treated with BMP4+FGF2 replica 2


title: 0400049I V1 day 21

description: PAXgene Sample


title: 0506178K V2 day 10

description: PAXgene Sample


title: 0470366D BL day 0

description: PAXgene Sample

value: BL


title: CTRL.4

value: female

value: Lung tumour


title: A4_EF_1: adult NCSs (ANS4) in EGF/FGF2 replica 1

value: Mouse Neural Stem Cell


title: A4_BF_1: adult NCSs (ANS4) treated with BMP4+FGF2 replica 1


title: CTRL.3


title: AD2_1_young


title: CTRL.5


title: CTRL.1


title: A4_B_1: adult NCSs (ANS4) treated with BMP4 replica 1


title: CTRL.2


title: C1: cervical cancer tissue

city: Foshan

first: Chenglai

last: Xia

address: Renming Xi  11#

institute: Affiliated Foshan Maternity & Chlid Healthcare Hospital, Southern Medical University

data_processing: The original image files of Illumina high-throughput sequencing were Base-Calling and transformed into original sequence sequences (Sequenced Reads) for subsequent analysis, that is, the collection of original sequences, called Raw Data; The analysis results are presented in FASTQ file (FQ for short). Based on the lncRNA length threshold, potential assembled transcripts shorter than 200 bp are filtered out. For the assembled transcripts with only one exon, the transcripts with FPKM ≥2 and those with multiple exons, the transcripts with FPKM ≥0.5 were kept. When the number of samples is more than 3, at least two samples are required to meet the screening criteria. The unknown transcripts are assembled by Stringtie software for further coding ability filtering, and CPC, CNCI and HMMER software are used for coding ability prediction FASTQC (v0.11.2) , fastp (v0.14.0) , Tophat (v2.0.13) , Lemma (v3.32.10) and Edger (v3.18.1) were used for quality control analysis.

source_name: cervical cancer patient

growth_protocol: The tumor tissue was removed and transferred to the laboratory in an ice box at low temperature.

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

treatment_protocol: After 3 times cleaning with PBS, the tumor tissue was stored in liquid nitrogen for further extraction of total RNA

tag: disease state

value: cervical cancer patient


title: C2: cervical cancer tissue


title: P3: cervical tissue

source_name: non-cervical cancer patient

value: non-cervical cancer patient


title: HEALTHY.2

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed. Reads were aligned to mouse genome build mm10 using HISAT2, v2.0.3beta aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR TMM method.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID

source_name: Lung

extract_protocol:
RNA from the Ly6g positive fractions was extracted using TRIzol (15596018, ThermoFisher Scientific).sequencing libraries, starting from 500 ng total RNA.
We performed SMARTer Stranded Total RNA-seq Pico v2 prep, starting from 2.44 ng RNA (batch1 samples) or 1ng RNA (batch2 samples), according to Takara protocol.

value: Lung Neutrophils

value: m

tag: status

value: Healthy

value: Lung

value: HEALTHY


title: HER2 L755S mutants grown in isolation

city: Baltimore

first: Swathi

last: Karthikeyan

state: MD

address: 733 N Broadway

institute: Johns Hopkins University School of Medicine

description: Control group

data_processing:
Data obtained was analysed using the GeneGlobe data analysis center from Qiagen according to the manufacturers instructions.
The average of 5 housekeeping genes  (ACTB, B2M, GAPDH, HPRT1, RPLP0) was used for normalization.
The GeneGlobe analyser software automatically performs average Ct, 2^(-Avg.(Delta(Ct)) and fold-change calculations from the uploaded raw threshold cycle data obtained from quadraplicates of each sample.
Matrix non-normalized worksheet shows the average (raw) Ct value calculated from quadraplicates of each sample, by GeneGlobe analyser
Matrix normalized worksheet shows the normalized signal or 2^(-Avg.(Delta(Ct)) computed by GeneGlobe analyzer;  Delta (Ct) =  (Ct(Gene of Interest) - Ave Ct(House Keeping Genes)).
Fold change worksheet shows the fold of change data obtained by comparing the Group 1 to the Control group.

label: SYBR Green

source_name: HER2 L755S isogenic cell line in MCF-10A background (grown in isolation)

label_protocol: cDNA was prepared using Qiagen RT2 first strand kit. It was followed by PCR Array

growth_protocol: The cells were grown in MCF-10A assay media (see materials and methods) in the absence of phenol red.

extract_protocol: RNA extraction was carried out using Rneasy Mini kit.

treatment_protocol:
The co-cultured cells (Group 1) were trypisinized and resuspended in PBS+3% charcoal dextran stripped FBS. Flow sorting was carried out at the Vanderbilt University Vantage core. Assay media with 20% charcoal dextran stripped FBS was used as catch buffer.
The control group was also put through the same trypisinization and flow-sorting procedure to maintain uniformity in treatment.

tag: culture condition

value: HER2 L755S was not co-cultured


title: C3: cervical cancer tissue


title: 0381134B V1 wk 0

description: PAXgene Sample

data_processing: The data were normalised using the neqc function with limma in R

value: HIV Positive

value: wk


title: HEALTHY.1

tag: gender

value: homozygous wt/wt


title: A4_B_2: adult NCSs (ANS4) treated with BMP4 replica 2


title: TAN.GLUT1KO.4

source_name: Lung tumour

value: Tumor Associated Neutrophils

value: f

value: Tumor bearing

tag: tissue

value: homozygous fl/fl


title: P2: cervical tissue


title: Co-cultured and flow-sorted HER2 L755S mutants

description: Group 1 (Test)

source_name: HER2 L755S isogenic cell line in MCF-10A background (co-cultured with PIK3CA E545K isogenic cell line in MCF-10A background and flow-sorted)

growth_protocol:
HER2 L755S mutants were co-cultured with the PIK3CA E545K mutants for 5 days.
The cells were grown in MCF-10A assay media (see materials and methods) in the absence of phenol red.

treatment_protocol:
The co-cultured cells (Group 1) were trypisinized and resuspended in PBS+3% charcoal dextran stripped FBS. Flow sorting was carried out at the Vanderbilt Flow Cytometry Shared Resource. Assay media with 20% charcoal dextran stripped FBS was used as catch buffer.
The control group was also put through the same trypisinization and flow-sorting procedure to maintain uniformity in treatment.

value: HER2 L755S was co-cultured


title: 0503022J BL wk 0

description: PAXgene Sample

value: BL


title: P1: cervical tissue


title: TAN.GLUT1KO.3

value: Lung tumour

tag: group


title: 0503022J V1 w 3

description: PAXgene Sample

tag: hiv status

value: w


title: TAN.GLUT1KO.2


title: TAN.GLUT1KO.1


title: NP_sssi [sanger AB 3730xl]

city: Geneva

first: victor

last: YTHIER

state: Geneva

address: Rue Michel-Servet,1

department: GEDEV

institute: University of Geneva

description:
percentage of methylation per CpG position
NP_sssi
NP_sssi_merge_mincov0.tab
NP_sssi_pm_mincov10.tab
model: sanger AB 3730xl

data_processing:
Bisulfite-Seq
Removing adaptater sequence using flexbar v3.4.0 (-r ${R2} -p ${R1} -b ${adapt} -bt 0.2 -be LEFT -qt 0)
Trimming using trim_galore v0.4.4 (qscore > 20), demultiplexing by barcode (0 missmatch) and UMI tagging (8 nt following barcode) using flexbar (-b ${bc} -bt 0.0 -be LEFT -qt 0  -t trimBC --umi-tags)
Filtering base on barcode-motif-barcode sequence using R v3.6.2 and BioString package v2.54.0 (0 missmatch fixed=FALSE)
Alignment on each reference sequence using bismark v0.20.0 (–non_directional -X 1000 -N 0 -q ref/${motif_name})
Filtering on nonCG conversion (ESC and NP only) (filter_non_conversion -p --percentage_cutoff 2)
UMI deduplication using umitools v0.5.5
Methylation extraction (bismark_methylation_extractor -p --no_overlap --bedGraph --cytosine_report --CX  --genome_folder  ref/${motif_name})
Genome_build: fr1 sequence with particular barcode-motif-barcode into beta globuline locus
Supplementary_files_format_and_content: tab-delimited text files include percentage of methylation for each library per Cell type and treatment …
RNA-Seq
Trimming using Trimmomatic v0.38 (ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Mapping using STAR v2.6.1b (--sjdbOverhang ${49})
Extract feature using featurecounts from Rsubread v1.6.2 (-T 6 -a GRCm38.89.gtf -F GTF -t exon -g gene_id -s 0)
EdgeR use v3.27.0
Genome_build: Ensembl – GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Cell Type

source_name: Embryonic Stem Cell differenciate into Neuronal Progenitor

extract_protocol:
cf paper
RNA-seq – Bisulfite-Seq – AmpBis-Seq - Sanger


title: TAN.CTRL.6


title: HepaRG_cell_acetaminophen_13mM_bile_acid_mix_3

tag: cell line

value: HepaRG cells

tag: treatment

value: APAP + BA


title: TAN.CTRL.5


title: 0470244A V1 wk 3

description: PAXgene Sample

tag: donor id

tag: timepoint


title: TAN.CTRL.4


title: 0504805L V2 wk 3

description: PAXgene Sample

tag: timepoint unit

tag: visit


title: ESC_untrt [sanger AB 3730xl]

description:
percentage of methylation per CpG position
ESC_untrt
ESC_untrt_merge_mincov0.tab
ESC_untrt_pm_mincov10.tab
model: sanger AB 3730xl

source_name: Embryonic Stem Cell


title: 0361442C V2 wk 5

description: PAXgene Sample

tag: age in years


title: WT mock-1h-rep2

city: Matsue-shi

first: Takahisa

last: Ogawa

state: Shimane

address: Nishikawatsu-cho 1060

country: Japan

institute: Shimane University

description: Gene expression data from 3-week-old WT rosette leaves after mock (water) treatment

hyb_protocol: Labeled cRNA was fragmented and hybridized to Affymetrix ATH1 GeneChip arrays for 16 h at 45°C according to Affymetrix protocols.

scan_protocol: Arrays were washed on an Affymetrix Fluidics Station 450 and measured for fluorescence intensity with an Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were processed using Affymetrix Gene Chip Operating Software (GCOS; Version 1.4.0.036).

organism: Arabidopsis thaliana

source_name: Three-week-old WT rosette leaves after mock treatment

label_protocol: Total RNA samples were reverse-transcribed, yielding double-strand cDNA, which was transcribed in vitro in the presence of biotin-labeled nucleotides with a 3' IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA), and purified.

growth_protocol: Wild-type Arabidopsis plants were grown on soil in a growth chamber kept at 23°C during 16 h of light (100 µmol/m2/s) and 8 h of darkness for 3 weeks.

extract_protocol: Total RNA was semi-automatically purified from various organs of Arabidopsis plants using a QuickGene RNA cultured cell Kit and QuickGene-Mini80 (FUJIFILM corporation, Tokyo, Japan). The quality and purity of the RNA were confirmed for microarray analysis with an Ultrospec 2100 pro (GE Healthcare UK Ltd, Amersham Place, England).

treatment_protocol: At 4 h after the illumination, detached rosette leaves of 3-week-old WT plants were floated on water (mock) or 0.1 mM FAD solution for 1h. After 1h, collected leaves were washed and used for microarray analysis.

tag: ecotype

value: rosette leaves

tag: age

value: mock (water)


title: 8502564L V1 wk 3

description: PAXgene Sample


title: 0503022J V2 ww 2

description: PAXgene Sample

value: ww


title: 0505135K BL day 0

description: PAXgene Sample

value: day


title: WT 0.1mM FAD-1h-rep1

description: Gene expression data from 3-week-old WT rosette leaves after 0.1 mM FAD treatment

source_name: Three-week-old WT rosette leaves after 0.1 mM FAD treatment

value: 0.1 mM FAD


title: TAN.CTRL.3

tag: cell type

tag: strain

tag: genotype


title: 0381378I V2 wk 2

description: PAXgene Sample

value: HIV Positive

value: wk


title: WT 0.1mM FAD-1h-rep2


title: 0730095D BL day 0

description: PAXgene Sample


title: 0372492G BL wk 0

description: PAXgene Sample


title: 0504866C V1 wk 3

description: PAXgene Sample


title: TAN.CTRL.1

value: Tumor Associated Neutrophils

value: m

tag: status

value: homozygous wt/wt


title: ATACseq_RBMX_KD2_2

city: NewYork

first: Zhaoqi

last: Liu

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

data_processing:
After alignment, MACS2 was applied with running mode ‘--broad’ to identify peaks.
Genome build: hg19
Output peaks from MACS2

source_name: MOLM13 cell line

growth_protocol: Leukemia cells were cultured in RPMI media (Cellgro) supplemented with 10% FBS, glutamine, and penicillin/streptomycin and grown at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated from MOLM13 cells 2 days after transduction with lentivirus expressing either control scramble shRNA or shRNAs targeting RBMX/L1 (shRNA1 and shRNA2) using TRIZOL and the RNeasy RNA extraction kit (n = 4 for each group).
RNA was denatured, and the first strand of cDNA was synthesized using oligo (dT)-primer-containing Illumina-compatible linker sequence. After removal of RNA, the second cDNA strand was synthesized with a random decamer containing another Illumina-compatible linker sequence. Illumina-compatible annealing sequences and external barcodes were introduced during amplification of the libraries.

treatment_protocol: MOLM13 cells were transduced by spinfection with lentivirus expressing either control scramble shRNA (Addgene #1864) or shRNAs targeting RBMX and RBMXL1 (shRNA1: GCCTATGTAAGGAAAGTGCTA and shRNA2: CGGTGGATATTCCATGAATTT) and 10 mg/ml polybrene at 1400 RPM for 1 hour. 1- or 2-days after transduction, depending on the cell line, cells were treated with 3 mg/ml puromycin.

value: MOLM13 cell line

value: RBMX/L1 knockdown


title: ATACseq_RBMX_KD2_3


title: WT mock-1h-rep1


title: ATACseq_RBMX_KD2_1


title: High_Fat_Diet_Adipose_Macrophages

first: Cecile

last: Benezech

address: 47 Little france Crescent

department: Centre for Cardiovascular Sciences

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.0.2.
Genome_build: mm10 (Ensembl 93)
Supplementary_files_format_and_content: fastq: fastq files of individual samples; mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: Epidymal adipose tissue

extract_protocol:
Enzymatic digestion and FACS
10X Genomics Single cell 3' gene expression V2

tag: disease status

value: Hight Fat Diet

tag: Sex

value: Male

value: CD45+Lin-Ly6Clow/-F4/80+ macrophage


title: Control_Diet_Adipose_Macrophages

description: 10X Genomics Single cell 3' gene expression V2

value: Unchallenged


title: 8501809A V2 wk 2

description: PAXgene Sample


title: ATACseq_RBMX_KD1_3


title: Caco2 infected with Encephalitizoon intestinalis [EI-3_S7]

city: Newark

last: Gao

state: NJ

address: 195 University Avenue

department: Biological Sciences

institute: Rutgers, the State University of New Jersey

data_processing:
Fastq files were analyzed using Partek® software. Copyright, Partek Inc. Partek and all other Partek Inc. product or service names are registered trademarks or trademarks of Partek Inc., St. Louis, MO, USA.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

growth_protocol: Cells werein 25 cm2 flasks in MEM containing 20% FBS, 1% penicillin-streptomycin (Thermo Fisher Scientific) at 37°C with 5% CO2.

extract_protocol:
RNA isolation was conducted using RNeasy Mini Kit (Qiagen, Catalog No. 74104) according to the manufacturer’s instructions.
The quality of RNA was first checked using Agilent 2200 TapeStation System (Agilent Technologies, Santa Clara, CA). All the RNA samples had an RNA integrity number (RIN) of >9.0 and were used for subsequent processing. The maximum recommended concentration was used as an input and they were subjected to oligo(dT)-based mRNA isolation using an NEBNext poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA). Illumina compatible RNAseq libraries were then prepared  using an NEBNext Ultra II RNA Library Prep Kit (New England BioLabs, Ipswich, MA). AMPureXP beads (Beckman Coulter, Brea, CA) were used to purify cDNA libraries. The quality and the size distribution of the libraries were determined by TapeStation and were  quantified using Qubit Fluorometer (Invitrogen). Barcoded libraries were pooled at equimolar ratios and sequenced on Illumina NextSeq 500 platform (Illumina, San Diego,CA) with 1×75 configuration.

treatment_protocol: Cells were infected with 100 μl of ∼10^6 spores/ml solution and maintained for 14 days.

tag: tissue source

value: Colon cancer tissue

tag: infectection status

value: Encephalitizoon intestinalis


title: 8501364E BL day 0

description: PAXgene Sample

tag: hiv status

value: BL


title: TAN.CTRL.2

tag: gender

value: Tumor bearing

tag: tissue

value: Lung tumour

tag: group


title: Caco2 infected with Encephalitizoon intestinalis [EI-1_S5]

tag: cell line


title: ATACseq_RBMX_KD1_2


title: Control Caco2 Uninfected [Control_4_S4]

source_name: Control Caco2 Uninfected


title: Control Caco2 Uninfected [Control_3_S3]


title: ATACseq_Control_3

value: wild type


title: 0360013A BL day 0

description: PAXgene Sample

value: HIV Positive

tag: donor id

tag: timepoint

tag: timepoint unit

value: day

tag: visit


title: 0422051G BL day 0

description: PAXgene Sample

tag: age in years


title: Control Caco2 Uninfected [Control_1_S1]


title: 0503291A BL wk 0

description: PAXgene Sample

value: wk


title: 0400444L BL day 0

description: PAXgene Sample


title: 0360047A V1 wk 3

description: PAXgene Sample


title: 0381130J BL wk 0

description: PAXgene Sample


title: ATACseq_Control_2


title: Caco2 infected with Encephalitizoon intestinalis [EI-2_S6]


title: ATACseq_Control_1


title: RNAseq_RBMX_KD2_4

data_processing:
Quality control for raw reads was performed using FastQC to make sure there were no major flaws in sequencing. Reads were then aligned to the hg19 assembly of the human genome using the STAR aligner. The resulting BAM files had their reads counted using the summarizeOverlaps function from the GenomicAlignments package in R. A count table of reads mapping to genes was constructed and a differential expression analysis was conducted using the DESeq software package. Prior to significance assessment, genes were filtered according to a reads per kilobase (RPK) value of 500 given the deep average depth of uniquely mapped reads (106,458,498) present in the samples. Statistical significance was determined with the negative binomial test using average read counts for controls and RBMX/RBMXL1 knockdown for all genes passing the RPK filter. The Benjamini-Hochberg correction was applied to all nominal p-values to account for multiple hypotheses testing to yield q-values. Genes were determined to be significantly differentially expressed if they possessed a q-value that was less than or equal to .05.
Genome build: hg19
excel, readcounts and deseq2


title: G_ros1_IM_R1

city: Porto Alegre

first: Catarine

last: Markus

address: Av. Bento Gonçalves, 7712

department: Department of Crop Science

country: Brazil

institute: Federal University of Rio Grande do Sul

data_processing:
Illumina HiSeq2500 sequencer with a requested sequencing depth of 18.7 million 100 bp single end reads per library.
RNA-seq raw reads were quality controlled using FASTQC (Version 0.10.1); Sequenced reads were trimmed with parameters: fastx_trimmer -f1 -l145 -m40
The protocol used for differential gene and transcript expression analysis of RNA-seq was described by Trapnell et al., (2012).
Genome_build: The libraries with sufficient quality were mapped to the corresponding reference genome A. thaliana TAIR10 (Lamesch et al., 2012) using bowtie2 and TopHat2 with default parameters (Trapnell et al., 2012; Kim et al., 2013).
Supplementary_files_format_and_content: Normalized abundance measurements - output table from cufflinks

source_name: leaf

growth_protocol: Plants were grown in a growth chamber (Percival) at 21°C during the day and 16°C during the night, relative humidity 70 – 75% and 150 µmol m-2 s-1 light intensity (16 h light/8 h dark).

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) according to the manufacture’s protocol and with an additional on-column DNase I digestion (Roche). RNA-seq libraries were made using Illumina TruSeq RNA Sample Prep Kit (San Diego/USA) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Plants were treated with 10.6 g ha-1 of imazethapyr, in addition of 0.5% v/v of Dash. Treated and non-treated plants were collected 48 h after application.

value: entire rosette of two plants

tag: age

value: three weeks old plants

tag: genotype/variation

tag: treatment

value: imazethapyr-treated


title: F_ros1_mock_R2

value: control


title: H_ros1_IM_R2


title: ATACseq_RBMX_KD1_1

value: MOLM13 cell line

tag: genotype

value: RBMX/L1 knockdown


title: RNAseq_RBMX_KD2_3


title: RNAseq_RBMX_KD2_2


title: D_WT_IM_R2

value: WT


title: Control Caco2 Uninfected [Control_2_S2]


title: RNAseq_RBMX_KD1_4


title: E_ros1_mock_R1


title: RNAseq_RBMX_KD1_3


title: RNAseq_RBMX_KD2_1


title: RNAseq_RBMX_KD1_2


title: C_WT_IM_R1


title: 0360013A V2 wk 2

last: Cameron

address: 10900 Euclid Ave

description: PAXgene Sample

source_name: Blood


title: 0504806I V2 wk 3

description: PAXgene Sample


title: B_WT_mock_R2


title: 0372492G V2 wk 2

description: PAXgene Sample


title: 0504169L V2 wk 2

description: PAXgene Sample


title: 0690972E BL day 0

description: PAXgene Sample


title: 8501932K BL day 0

description: PAXgene Sample


title: 8502572C V2 day 10

description: PAXgene Sample


title: RNAseq_RBMX_KD1_1


title: 0361442C BL day 0

description: PAXgene Sample


title: 0280750I V2 wk 2

description: PAXgene Sample


title: RNAseq_Control_3


title: RNAseq_Control_2


title: RNAseq_Control_4


title: RNAseq_Control_1


title: LN1-1 pLKO-GFP

city: Miaoli County

first: Ya-Wen

last: Chen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description: Vector control

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalization.

source_name: Human oral squamous cel carcinoma cell line

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-G Bioti- aRNA Labeling kit (Epicentre) for Illumina arrays.

growth_protocol: Cells were cultured in RPMI medium with 10% FBS at 37°C in an incubator containing 5% CO2.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

value: Vector control cells


title: 0370121L BL day 0

city: Cleveland

first: Mark

institute: Case Western Reserve University

description: PAXgene Sample


title: 76-1

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were mapped to the mouse genome (mm10) using HISAT2
Reads were counted using HTSeq-count (v0.6.0) against ENCODE annotations, release 90.
Differential gene expression between samples of different conditions was determined using the DESeq2 package (v1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Brain

extract_protocol:
RNA was isolated (gfapCre+ EAAT2Δ/+, n = 6; gfap-Cre− EAAT2+/+, n = 6; syn-Cre+ EAAT2−/−, n = 6; syn-Cre− EAAT2+/+, n = 6 mice) using a RNeasy Lipid Tissue Mini Kit (Qiagen). Quality of RNA samples was determined using a bioanalyzer (Agilent).
Samples for RNA-Seq with RNA integrity number values >9. 500 ng of purified RNA were used to prepare sequencing libraries according to the Illumina protocol and sequenced with an Illumina HiSeq 2500 system.

tag: cell type

value: GFAP


title: Setdb2 KO

city: New Haven

first: Xinbo

last: Zhang

state: Connecticut

address: Rm320, 10 Amistad St

department: Comparative Medicine

institute: Yale University

data_processing:
Reads were aligned against mouse genome mm9 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 5% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Genome_build: mmp9
Supplementary_files_format_and_content: Cell-gene-barcode matrices

source_name: CD45+ Cell

growth_protocol: Bone Marrow (BM) cells were obtained by flushing the  tibias and femurs of age-matched (8-week-old) wild type (WT) or Setdb2-/- mice. The transplantation was done in Ldlr-/- mice lethally irradiated with 5 Gy two times in series and  intravenously infused with 2 millions donor BM cells each mouse.

extract_protocol:
Atherosclerotic aorta was digested with 1 mg/ml Collagenase  A for 7 min (Roche, Cat 11088785103) at 37 °C to remove the adventitia under microscope. Aortic tissue  was cut into small pieces and subjected to enzymatic digestion with 1.5 mg/ml Collagenase A and 0.5  mg/ml Elastase (Worthington, Cat LS006365) for 40 min at 37 °C while shaking. Viable CD45+  cells were sorted by FACS Aria III (BD Biosciences) with gating on live, single cells using ive/dead viability dye eFluor 450  (Thermo Fisher Scientific).
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using the V2 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

treatment_protocol: Animals were maintained in a Western-type diet for 16 weeks.

tag: strain

value: Ldlr-/-

value: Aorta

value: Western diet for 16 weeks


title: WT


title: Osmr KO rep3

city: Guangzhou

first: Jun

state: Guangdong

address: No.2 Lujing Road

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Epidermal keratinocytes

extract_protocol:
Epidermal keratinocytes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epidermal keratinocytes

value: post natal day 30

value: Osmr-/-


title: Osmr KO rep2


title: TP15, exosome, non coding small RNA seq

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

data_processing:
1) Getting rid of low quality tag (The criteria for this is listed in the explanation of meaning of each
row in the result table)
2) Getting rid of tag with 5' primer contaminants
3) Getting rid of tag without 3' primer
4) Getting rid of tag without the insert
5) Getting rid of tag with poly A
6) Getting rid of tag shorter than 18nt
7) Summarize the length distribution of the clean tags
After filtering, the remaining tags are called "clean tags" and stored as FASTQ format \[7\] (see FASTQ Format in help page).
Data was processed via miRDeep2.
First, fastq file was mapped to hg38 genome using mapper.pl as
mapper.pl LP01.fq -n -h -g hsa -e -n -i -j -k AGATCGGAAGAGCACACGTCT -l 18 -m -s LP01.fastq.collapsed -p ~/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/genome -t LP01_vs_genome_h38.arf
Then it was processed via miRDeep2.pl as
miRDeep2.pl LP01.fastq.collapsed ~/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/genome.fa LP01_vs_genome_h38.arf   ~/miRBase/mature_human.fa ~/miRBase/mature_chimp.fa ~/miRBase/hairpin_human.fa -t has
Genome_build: hg38
Supplementary_files_format_and_content: csv file reports output from miRDeep2

source_name: exosome

extract_protocol:
Total RNA was extracted by RNeasy mini kit (Qiagen).
1) Filter Small RNA: Separate RNA segment of different size by PAGE gel,select 18-30nt stripe and recycle. 2) Adaptor  ligation: Prepare connection system, blend and centrifuge, connect warmly for a period of time. 3) RT-PCR: Prepare  reverse transcription system, connect warmly for a period on PCR on PCR instrument, then PCR amplification. 4) Purify  PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recylced products in EB solution. Finally,  label to finish the library construction. 5) Library quality testing: Use Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-  TimePCR System to test quality and production of the prepared library.

treatment_protocol: Exosome rich fraction was extracted by Exoquick (System Biosciences).

tag: disease state

value: tuberculosis

tag: sample type

value: exosome


title: TP16, exosome, non coding small RNA seq


title: 74-3


title: A_WT_mock_R1

value: entire rosette of two plants


title: Osmr WT rep1


title: Osmr KO rep1


title: Osmr WT rep3


title: 75-1


title: TP14, exosome, non coding small RNA seq


title: Osmr WT rep2


title: UCB 2

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
Sequencing was done using 100-cycle paired read protocol and multiplexing to obtain ~40 million reads/sample.
Samples were aligned to GRCh38 using HISAT2 2.1.
Read counts were calculated using HTSeq 0.10.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files with read counts.

source_name: Wild-type_In vitro derived CD4+CD8+ T-cells

growth_protocol: MACS-purified CD34+ cells were counted and seeded at a density of 50,000-200,000 cells per 6-well plate in vitro, and differentiated towards the T-cell lineage by co-culture with OP9-DL4-7FS cells in OP9 medium at 37oC, 5% CO2, and T-cell progenitors were passaged and co-cultured with fresh OP9-DL4-7FS cells approximately every 5 days.

extract_protocol:
Total RNA was extracted from the sorted CD4+CD8+ DP cell populations using TRIzol.
Library construction was done using Illumina Novaseq 6000, with Illumina TruSeq Strandard Total RNA Sample Preparation kit.

tag: tissue origin

value: Human umbilical cord blood

value: Wild-type

value: In vitro derived CD4+CD8+ T-cells


title: Yeast_pGAL_PRP43_Glu_B

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Reads were mapped against yeast rDNA and snoRNAs from the SGD database (https://www.yeastgenome.org/)
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

organism: Saccharomyces cerevisiae

source_name: Whole cell RNA from yeast

growth_protocol: Yeast strains used in this study are listed in Supplementary Table S3 and were grown in YPD/G (1% yeast extract, 2% peptone, 2% glucose/galactose) or synthetic media lacking leucine where appropriate.

extract_protocol:
Whole cell RNA was extracted from exponentially growing yeast cells using acidic phenol and chloroform extraction
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

tag: tissue

value: Yeast culture


title: Yeast_pGAL_PRP43_Gal_B


title: LN1-1 IGFBP3 sh5

description: IGFBP3 shRNA expression

value: IGFBP3 knockdown


title: Yeast_pGAL_PRP43_Glu_A


title: 0730166B V2 wk 2

description: PAXgene Sample

extract_protocol: Total RNA was extracted using Qiagen's PreAnalytix PAXgene Blood RNA kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Globin removal was conducted with ThermoFisher's GLOBINclear kit. Quality control was performed with Bio-Rad's Experion.

tag: hiv status

value: HIV Positive

value: wk


title: 0730028D V2 wk 2

description: PAXgene Sample


title: 74-1

value: GFAP


title: Yeast_Delta_Dbp3_A


title: Yeast_Delta_Dbp3_B


title: UCB 1


title: 71-5


title: TP12, exosome, non coding small RNA seq


title: TP11, exosome, non coding small RNA seq


title: 75-2


title: TP10, exosome, non coding small RNA seq


title: 72-1


title: KO4 TCRbeta-Transduced

source_name: RAG2-KO TCRbeta-transduced_In vitro derived CD4+CD8+ T-cells

value: Human embryonic stem cells

value: RAG2-KO TCRbeta-transduced


title: 71-4


title: Yeast_WT_A

value: WT


title: Yeast_pGAL_PRP43_Gal_A


title: 71-2


title: TP13, exosome, non coding small RNA seq


title: 72-4


title: Yeast_WT_B


title: TP09, exosome, non coding small RNA seq


title: KO4 1

source_name: RAG2-KO_In vitro derived CD4+CD8+ T-cells


title: KO1 TCRbeta-Transduced


title: KO4 2


title: TP06, exosome, non coding small RNA seq


title: TP07, exosome, non coding small RNA seq


title: 76-2


title: Suv39h_KO_HiC

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

data_processing:
Hi-C data processing was done by using Docker for 4DN Hi-C pipeline (v43
After filtering valid Hi-C alignments, .hic format Hi-C matrix files were generated by Juicer Tools
The A/B compartment profiles in 100-kb bins were calculated from .hic format HiC matrix files (intrachromosoma KR normalized Hi-C maps) by Juicer Tools
Genome_build: mm10
Supplementary_files_format_and_content: Text format data of eigen vector

source_name: mouse embryonic stem cells

growth_protocol: mESCs were maintained in DMEM with 1%FCS/10%KSR/LIF on gelatin coated dish.

extract_protocol:
Hi-C experiments were performed, based on DpnII enzyme
Library was constructed as previously described doi: 10.1038/s41467-018-03748-1

treatment_protocol: We treated 800 nM 4-OHT for 5 days to Setdb1 conditional KO mESCs to deplete SETDB1. We treated 2uM UNC0642 for 3 days to mESCs to inhibit G9a/GLP catalytic activity.

value: ADF157 Suv39h1/2 DKO mES

value: mouse embryonic stem cells


title: TP08, exosome, non coding small RNA seq


title: Suv39h_KO_UNC_HiC

value: 2uM UNC642 for 3 days


title: 71-1


title: TP05, exosome, non coding small RNA seq

value: tuberculosis


title: 52-4

value: Syn


title: 52-3


title: Suv39h_UNC_HiC

value: ADF1-26 WT mES


title: Suv39h_WT_HiC


title: Control WT 2


title: KO1 2


title: TP04, exosome, non coding small RNA seq

value: exosome


title: 50-4


title: Setdb1_KO_UNC_HiC

value: #33-6 Setdb1 conditional KO mES

value: 800nM 4-OHT for 2 days then 2uM UNC0642 for 3 days


title: 52-2


title: TP03, exosome, non coding small RNA seq


title: Setdb1_KO_HiC

value: 800nM 4-OHT for 5 days


title: Control WT 1

value: Wild-type

value: In vitro derived CD4+CD8+ T-cells


title: TP02, exosome, non coding small RNA seq


title: Setdb1_UNC_HiC


title: TP01, exosome, non coding small RNA seq


title: Unstimulated Malian Adults [R25]

city: Rockville

first: Rajan

last: Guha

address: 5625 Fishers Lane,Room No:4N07

institute: NIAID/NIH

data_processing:
Quality control using FASTQC
Trimming was performed using cutadapt
Alignment was performed using STAR aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene counts were generated using featureCounts

source_name: Unstimulated Malian Adults

growth_protocol: Monocytes were cultured in complete RPMI (RPMI 1640 plus 10% human AB serum, 1% penicillin/streptomycin), at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Cells were isolated and kept in RNAprotect buffer (Qiagen) at -80 degree before RNA was isolated from the samples. RNA was isolated using RNAeasy kit according to manufacturer’s instruction. Isolated RNA’s were checked for quality and quantified using Agilient Bioanalyzer. RNA’s with RIN values greater than 7 were used for all the analysis.
cDNA was prepared from 10 ng total RNA using the Ovation® RNA Seq System V2 (Tecan) according to manufacturer’s instructions.  This method employs both poly-T and random primers so that both poly-adenylated and non-poly-adenylation messages are included.  The cDNA product was end-repaired using the NEBNext End Repair Module (New England Biolabs). RNA-Seq libraries were prepared using 1 g of end-repaired cDNA using the TruSeq Stranded RNA Kit (Illumina), however due to the method of amplification the libraries are not stranded.  Unique dual-indexed barcode adapters were applied to each library. Libraries were pooled in an equimolar ratio for sequencing.  The pooled libraries were sequenced on one lane of an S4 flow cell on a NovaSeq 6000 using version 1 chemistry to achieve a minimum of 49 million 150 base read pairs.  The data was processed using RTA version 3.4.4 and BWA-0.7.12.

treatment_protocol: Monocytes were stimulated in a ratio of 5 pf-iRBC per monocytes,control monocytes were kept in the same medium without Pf-iRBC.Monocytes were harvested after 24 hrs of incubation and proceed for downstream RNA isolation.

tag: subect status

value: Unstimulated Malian Adults

value: monocytes


title: 50-1


title: Unstimulated Malian Adults [R11]


title: 0360013A V1 wk 3

description: PAXgene Sample

data_processing: The data were normalised using the neqc function with limma in R

value: HIV Positive

tag: donor id

value: wk


title: KO1 1

value: Human embryonic stem cells


title: Unstimulated Malian Adults [R10]


title: 49-2


title: 48-4


title: LP13, exosome, non coding small RNA seq

value: latent tuberculosis


title: LP12, exosome, non coding small RNA seq


title: Unstimulated Malian Adults [R9]


title: 50-3


title: Pf-iRBC stimulated-Malian Adult [R8]

source_name: Pf-iRBC stimulated-Malian Adult

value: Pf-iRBC stimulated-Malian Adult


title: Pf-iRBC stimulated-Malian Adult [R7]


title: LP16, exosome, non coding small RNA seq


title: 47-4


title: 48-1


title: Pf-iRBC stimulated-Malian Adult [R6]


title: Setdb1_KO_Input_rep1

data_processing:
Adaptor sequences in reads were trimmed using Trim Galore version 0.3.7
Trimmed reads were aligned to the mm10 genome build using bowtie version 0.12.7
Duplicated reads were removed using samtools version 0.1.18
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

growth_protocol: mESCs were maintained in DMEM with 1%FCS/10%KSR/LIF on gelatin coated dish. iMEFs were maintained in DMEM with 10% FCS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30seconds off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) or SMARTER ThruPLEX DNA-seq kit (TAKARA) and SMARTer DNA Unique Dual Index Kit (TAKARA) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS).

treatment_protocol: We treated 800 nM 4-OHT for 5 days to Setdb1 conditional KO mESCs to deplete SETDB1. We treated 2uM UNC0642 for 3 days and 5 days to mESCs and iMEFs, respectively to inhibit G9a/GLP catalytic activity.

value: mouse embryonic stem cells

tag: antibody


title: TT2_Input_rep1

value: TT2 mES


title: Setdb1_WT_iMEF_Input_rep1

source_name: immortalized mouse embryonic fibroblast

value: 3-12#13 Setdb1 KO iMEF

value: immortalized mouse embryonic fibroblast


title: Setdb1_KO_UNC_H3K9me3

value: 2F3 anti-H3K9me3


title: Setdb1_KO_H3K9me3

value: #33-6 Setdb1 conditional KO mES


title: LP11, exosome, non coding small RNA seq

value: exosome


title: Setdb1_UNC_H3K9me3

value: 2uM UNC642 for 3 days


title: 47-5

value: Syn


title: LP15, exosome, non coding small RNA seq


title: LP14, exosome, non coding small RNA seq


title: Setdb1_WT_H3K9me3


title: Pf-iRBC stimulated-Malian Adult [R5]


title: Pf-iRBC stimulated-Malian Adult [R4]


title: Pf-iRBC stimulated-Malian Adult [R3]


title: 48-3


title: P8-4

city: Minneapolis

first: Marc

middle: Kevin

last: Jenkins

state: Minnesota

address: 2101 Sixth St. SE

department: Center for Immunology

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via hisat2 (2.1.0) using the mouse genome (mm10) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

growth_protocol: Not applicable, in vivo samples.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus micro spin column purification kit.
RNA libraries were prepared for sequencing using Takara Pico Mammalian (ribo-depletion) protocols

treatment_protocol: Se infection

value: 12 weeks

value: Spleen and lymph nodes

value: LpdAp:I-Ab-specific T cells

value: 30 d after S. enterica infection


title: P8-2


title: LP09, exosome, non coding small RNA seq


title: 6P9

source_name: 6P9 (CXCR3)


title: LP08, exosome, non coding small RNA seq


title: 72h_after_UNC0642_removal_H3K9me2

value: 6D11 anti-H3K9me2

value: 72h_after_2uM UNC0642 treatment for 3 days


title: LP07, exosome, non coding small RNA seq

value: latent tuberculosis


title: LP10, exosome, non coding small RNA seq


title: Setdb1_WT_HiC


title: Pf-iRBC stimulated-Malian Adult [R2]

value: Pf-iRBC stimulated-Malian Adult

value: monocytes


title: 64h_after_UNC0642_removal_H3K9me2

value: TT2 mES

value: mouse embryonic stem cells

value: 64h_after_2uM UNC0642 treatment for 3 days


title: 1P9

source_name: 1P9 (CXCR3)


title: 48h_after_UNC0642_removal_H3K9me2

value: 48h_after_2uM UNC0642 treatment for 3 days


title: 56h_after_UNC0642_removal_H3K9me2

value: 56h_after_2uM UNC0642 treatment for 3 days


title: Pf-iRBC stimulated-Malian Children [R19]

source_name: Pf-iRBC stimulated-Malian Children

value: Pf-iRBC stimulated-Malian Children


title: 4P9

source_name: 4P9 (CXCR3)


title: LP06, exosome, non coding small RNA seq

value: exosome


title: LP05, exosome, non coding small RNA seq


title: 4P11


title: Pf-iRBC stimulated-Malian Children [R17]


title: Pf-iRBC stimulated-Malian Children [R18]


title: LP03, exosome, non coding small RNA seq


title: 5P9

source_name: 5P9 (CXCR3)


title: Pf-iRBC stimulated-Malian Children [R16]


title: mRNA_LV_PS_9564

city: Stanford

first: Hyun Tae

middle: V

last: Hwang

address: 300 Pasteur Dr. S242

institute: Stanford University

data_processing:
FastQC (v0.11.5) was used to assess read quality.
Reads were mapped to mouse reference genome mm9 using STAR (v2.5.3a) with UCSC gene annotations using default conditions as described in Dobin et al., Bioinformatics, 2013.
Normalized transcript abundances (FPKM) were calculated and differential expression analyses for RNA-Seq were performed using the Cuffdiff program from the Cufflinks v2.2.1 suite using default conditions as described in Trapnell et al., Nature Biotechnology, 2013. The bias detection and correction algorithm was used to significantly improve accuracy of transcript abundance estimates as described in Roberts et al., Genome Biology, 2011. The initial estimation procedure was used to more accurately weight reads mapping to multiple locations in the genome.
Exploration, analysis and visualization of Cuffdiff results were performed using the CummeRbund v2.16.0 R package installed in R v3.3.1 as described in Trapnell et al., Nature Protocols, 2012.
Pathway and gene ontology (GO) analyses were carried out through Advaita Bioinformatics (Ann Arbor, MI).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Heart tissue

growth_protocol: Male FVB mice aged between 10-13 weeks were used.

extract_protocol:
Total RNA from murine right and left ventricles were isolated using miRNeasy Mini Kit (217004; Qiagen, Germantown, MD) following the manufacturer's guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RV failure was induced by pulmonary artery banding. Sham-operated controls were also generated.

value: Left ventricular free wall

value: FVB

tag: developmental stage

value: Adult

tag: Sex

value: Male

value: PS


title: 24h_after_UNC0642_removal_H3K9me2

value: 6D11 anti-H3K9me2

value: 24h_after_2uM UNC0642 treatment for 3 days


title: Pf-iRBC stimulated-Malian Adult [R1]


title: LP04, exosome, non coding small RNA seq

value: latent tuberculosis


title: Pf-iRBC stimulated-Malian Children [R15]


title: Setdb1_KO_UNC_iMEFs_H3K9me2_rep2

value: 3-12#13 Setdb1 KO iMEF

value: immortalized mouse embryonic fibroblast

value: 2uM UNC0642 for 5 days


title: 0h_after_UNC0642_removal_H3K9me2

value: TT2 mES

value: mouse embryonic stem cells

value: 2uM UNC0642 for 3 days


title: Pf-iRBC stimulated-Malian Children [R20]

value: monocytes