title: RNA-Seq single cell_CKp25_1w_m1_B8


title: RNA-Seq single cell_CKp25_1w_m1_B3

status: Public on Oct 10 2017

type: SRA

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

country: USA

institute: MIT

library_source: transcriptomic

data_processing:
The raw fastq data of 40-bp paired-end sequencing reads were aligned to the mouse mm9 reference genome using TopHat2.0.
The mapped reads were processed by Cufflinks 2.2 with UCSC mm9 reference gene annotation to estimate transcript abundances.
Genome_build: mm9
Supplementary_files_format_and_content: Text table format for gene expression FPKM values.

molecule: total RNA

organism: Mus musculus

extract_protocol:
Hippocampal tissue was enzymatically digested using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, catalogue number 130-092-628) according to the manufacturer’s protocol.
FACS sorted single cell lysis in 96-well plates were subject to Smart-seq2 RNA library preparation. A QC step was performed to check amplification of the libraries before multiplexing for sequencing.
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter, catalogue number A63987) before oligo-dT primed reverse transcription with Maxima H Minus Reverse Transcriptase (Thermo Fisher, catalogue number EP0753), which was followed by 21 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, catalogue number KK2602).
Libraries were tagmented using the Nextera XT DNA Library Preparation Kit (Illumina, catalogue number FC-131-1096) and the Nextera XT Index Kit v2 Sets A,B,C, and D according to the manufacturer’s instructions with minor modifications.

tag: strain

tag: age

value: 3 months and 1 week

tag: cell type

value: isolated, FACS sorted single hippocampal microglia


title: RNA-Seq single cell_CKp25_1w_m1_B4


title: RNA-Seq single cell_CKp25_1w_m1_B6


title: RNA-Seq single cell_CKp25_1w_m1_B2


title: RNA-Seq single cell_CKp25_1w_m1_A12


title: RNA-Seq single cell_CKp25_1w_m1_A10


title: RNA-Seq single cell_CKp25_1w_m1_B1


title: RNA-Seq single cell_CKp25_1w_m1_A9


title: RNA-Seq single cell_CKp25_1w_m1_A11


title: RNA-Seq single cell_CKp25_1w_m1_A8


title: RNA-Seq single cell_CKp25_1w_m1_A4


title: RNA-Seq single cell_CKp25_1w_m1_E5


title: RNA-Seq single cell_CKp25_1w_m1_A7


title: RNA-Seq single cell_CKp25_1w_m1_A5


title: RNA-Seq single cell_CKp25_1w_m1_C2


title: RNA-Seq single cell_CKp25_1w_m1_A1


title: RNA-Seq single cell_CKp25_1w_m1_A3


title: RNA-Seq single cell_CK_1w_m1_H9

value: CK


title: RNA-Seq single cell_CK_1w_m1_H12


title: RNA-Seq single cell_CK_1w_m1_H11


title: RNA-Seq single cell_CK_1w_m1_H7


title: RNA-Seq single cell_CK_1w_m1_H10


title: RNA-Seq single cell_CK_1w_m1_H5


title: RNA-Seq single cell_CK_1w_m1_H3


title: RNA-Seq single cell_CK_1w_m1_G12


title: RNA-Seq single cell_CK_1w_m1_H4


title: RNA-Seq single cell_CK_1w_m1_H8


title: RNA-Seq single cell_CK_1w_m1_H6


title: RNA-Seq single cell_CK_1w_m1_H2


title: RNA-Seq single cell_CK_1w_m1_G10


title: RNA-Seq single cell_CK_1w_m1_G11


title: RNA-Seq single cell_CK_1w_m1_G8


title: RNA-Seq single cell_CK_1w_m1_H1


title: RNA-Seq single cell_CK_1w_m1_G7


title: RNA-Seq single cell_CK_1w_m1_G4


title: RNA-Seq single cell_CK_1w_m1_G9


title: RNA-Seq single cell_CKp25_1w_m1_A6


title: RNA-Seq single cell_CK_1w_m1_G3


title: RNA-Seq single cell_CK_1w_m1_G5


title: RNA-Seq single cell_CKp25_1w_m1_A2


title: RNA-Seq single cell_CK_1w_m1_F10


title: RNA-Seq single cell_CK_1w_m1_G2


title: RNA-Seq single cell_CK_1w_m1_F5


title: RNA-Seq single cell_CK_1w_m1_F11


title: RNA-Seq single cell_CK_1w_m1_G1


title: RNA-Seq single cell_CK_1w_m1_F2


title: RNA-Seq single cell_CK_1w_m1_F1


title: RNA-Seq single cell_CK_1w_m1_G6


title: RNA-Seq single cell_CK_1w_m1_F6


title: RNA-Seq single cell_CK_1w_m1_F12


title: RNA-Seq single cell_CK_1w_m1_E10


title: RNA-Seq single cell_CK_1w_m1_F9


title: RNA-Seq single cell_CK_1w_m1_F3


title: RNA-Seq single cell_CK_1w_m1_E9


title: RNA-Seq single cell_CK_1w_m1_E12


title: RNA-Seq single cell_CK_1w_m1_F8


title: RNA-Seq single cell_CKp25_1w_m1_H6


title: RNA-Seq single cell_CK_1w_m1_F4


title: RNA-Seq single cell_CK_1w_m1_E6


title: RNA-Seq single cell_CK_1w_m1_E5


title: RNA-Seq single cell_CK_1w_m1_E4


title: RNA-Seq single cell_CK_1w_m1_E8


title: RNA-Seq single cell_CK_1w_m1_E3


title: RNA-Seq single cell_CK_1w_m1_F7


title: RNA-Seq single cell_CK_1w_m1_D10


title: RNA-Seq single cell_CK_1w_m1_E7


title: RNA-Seq single cell_CK_1w_m1_D11


title: RNA-Seq single cell_CK_1w_m1_E1


title: RNA-Seq single cell_CK_1w_m1_E2


title: RNA-Seq single cell_CK_1w_m1_D8


title: RNA-Seq single cell_CK_1w_m1_E11


title: RNA-Seq single cell_CK_1w_m1_D7


title: RNA-Seq single cell_CK_1w_m1_D3


title: RNA-Seq single cell_CK_1w_m1_D5


title: RNA-Seq single cell_CK_1w_m1_D1


title: RNA-Seq single cell_CK_1w_m1_D12


title: RNA-Seq single cell_CK_1w_m1_C12


title: RNA-Seq single cell_CK_1w_m1_C9


title: RNA-Seq single cell_CK_1w_m1_C4


title: RNA-Seq single cell_CK_1w_m1_C5


title: RNA-Seq single cell_CK_1w_m1_C2


title: RNA-Seq single cell_CK_1w_m1_C10


title: RNA-Seq single cell_CK_1w_m1_C8


title: RNA-Seq single cell_CK_1w_m1_D4


title: RNA-Seq single cell_CK_1w_m1_C11


title: RNA-Seq single cell_CK_1w_m1_C1


title: RNA-Seq single cell_CK_1w_m1_D6


title: RNA-Seq single cell_CK_1w_m1_D9


title: RNA-Seq single cell_CK_1w_m1_B11


title: RNA-Seq single cell_CK_1w_m1_B9


title: RNA-Seq single cell_CK_1w_m1_B12


title: RNA-Seq single cell_CK_1w_m1_B8


title: RNA-Seq single cell_CK_1w_m1_B10


title: RNA-Seq single cell_CK_1w_m1_C6


title: RNA-Seq single cell_CK_1w_m1_C7


title: RNA-Seq single cell_CK_1w_m1_B6


title: RNA-Seq single cell_CK_1w_m1_C3


title: RNA-Seq single cell_CK_1w_m1_B3


title: RNA-Seq single cell_CK_1w_m1_B5


title: RNA-Seq single cell_CK_1w_m1_B7


title: RNA-Seq single cell_CK_1w_m1_B4


title: RNA-Seq single cell_CK_1w_m1_B1


title: RNA-Seq single cell_CK_1w_m1_B2


title: RNA-Seq single cell_CK_1w_m1_A11


title: RNA-Seq single cell_CK_1w_m1_D2


title: RNA-Seq single cell_CK_1w_m1_A12


title: RNA-Seq single cell_CK_1w_m1_A7


title: RNA-Seq single cell_CK_1w_m1_A8


title: RNA-Seq single cell_CK_1w_m1_A9


title: RNA-Seq single cell_CK_1w_m1_A6


title: RNA-Seq single cell_CK_1w_m1_A5


title: RNA-Seq single cell_CK_1w_m1_A4


title: RNA-Seq single cell_CK_1w_m1_A1


title: RNA-Seq single cell_CK_1w_m1_A2


title: RNA-Seq single cell_CKp25_2w_m2_H11

value: 3 months and 2 weeks


title: RNA-Seq single cell_CKp25_2w_m2_H10


title: RNA-Seq single cell_CKp25_2w_m2_H12


title: RNA-Seq single cell_CK_1w_m1_A3


title: RNA-Seq single cell_CKp25_2w_m2_H8


title: RNA-Seq single cell_CKp25_2w_m2_H6


title: RNA-Seq single cell_CKp25_2w_m2_H9


title: RNA-Seq single cell_CKp25_2w_m2_H5


title: RNA-Seq single cell_CKp25_2w_m2_H7


title: RNA-Seq single cell_CKp25_2w_m2_H3


title: RNA-Seq single cell_CKp25_2w_m2_H4


title: RNA-Seq single cell_CKp25_2w_m2_H2


title: RNA-Seq single cell_CKp25_2w_m2_G12


title: RNA-Seq single cell_CKp25_2w_m2_H1


title: RNA-Seq single cell_CKp25_2w_m2_G11


title: RNA-Seq single cell_CKp25_2w_m2_G10


title: RNA-Seq single cell_CKp25_2w_m2_G8


title: RNA-Seq single cell_CK_1w_m1_A10


title: RNA-Seq single cell_CKp25_2w_m2_G7


title: RNA-Seq single cell_CKp25_2w_m2_G6


title: RNA-Seq single cell_CKp25_2w_m2_G4


title: RNA-Seq single cell_CKp25_2w_m2_G5


title: RNA-Seq single cell_CKp25_2w_m2_G2


title: RNA-Seq single cell_CKp25_2w_m2_G1


title: RNA-Seq single cell_CKp25_2w_m2_G3


title: RNA-Seq single cell_CKp25_2w_m2_F11


title: RNA-Seq single cell_CKp25_2w_m2_F10


title: RNA-Seq single cell_CKp25_2w_m2_F8


title: RNA-Seq single cell_CKp25_2w_m2_F4


title: RNA-Seq single cell_CKp25_2w_m2_F6


title: RNA-Seq single cell_CKp25_2w_m2_F3


title: RNA-Seq single cell_CKp25_2w_m2_F7


title: RNA-Seq single cell_CKp25_2w_m2_F2


title: RNA-Seq single cell_CKp25_2w_m2_F5


title: RNA-Seq single cell_CKp25_2w_m2_E11


title: RNA-Seq single cell_CKp25_2w_m2_E12


title: RNA-Seq single cell_CKp25_2w_m2_F1


title: RNA-Seq single cell_CKp25_2w_m2_G9


title: RNA-Seq single cell_CKp25_2w_m2_E8


title: RNA-Seq single cell_CKp25_2w_m2_E7


title: RNA-Seq single cell_CKp25_2w_m2_E10


title: RNA-Seq single cell_CKp25_2w_m2_E5


title: RNA-Seq single cell_CKp25_2w_m2_E9


title: RNA-Seq single cell_CKp25_2w_m2_E6


title: RNA-Seq single cell_CKp25_2w_m2_E3


title: RNA-Seq single cell_CKp25_2w_m2_E4


title: RNA-Seq single cell_CKp25_2w_m2_E2


title: RNA-Seq single cell_CKp25_2w_m2_F12


title: RNA-Seq single cell_CKp25_2w_m2_E1


title: RNA-Seq single cell_CKp25_2w_m2_D11


title: RNA-Seq single cell_CKp25_2w_m2_D12


title: RNA-Seq single cell_CKp25_2w_m2_D9


title: RNA-Seq single cell_CKp25_2w_m2_D5


title: RNA-Seq single cell_CKp25_2w_m2_D6


title: RNA-Seq single cell_CKp25_2w_m2_D3


title: RNA-Seq single cell_CKp25_2w_m2_D7


title: RNA-Seq single cell_CKp25_2w_m2_D1


title: RNA-Seq single cell_CKp25_2w_m2_C12


title: RNA-Seq single cell_CKp25_2w_m2_D8


title: RNA-Seq single cell_CKp25_2w_m2_D4


title: RNA-Seq single cell_CKp25_2w_m2_D2


title: RNA-Seq single cell_CKp25_2w_m2_C10


title: RNA-Seq single cell_CKp25_2w_m2_C11


title: CD3/28_24h_2

city: Yokohama

first: Takayuki

last: Imanishi

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences (IMS)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: helper T cell_CD3/28_24h

extract_protocol:
RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: spleen

value: 12 weeks

tag: genotype

value: wild type

value: helper T cell; CD4+ T cells

tag: stimulated with

value: anti-CD3/28 for 24hrs


title: CD3/28+cGAMP_24h_2

source_name: helper T cell_CD3/28+cGAMP_24h

value: anti-CD3/28+cGAMP for 24hrs


title: RNA-Seq single cell_CKp25_2w_m2_C7


title: RNA-Seq single cell_CKp25_2w_m2_C8


title: CD3/28+cGAMP_24h_1


title: RNA-Seq single cell_CKp25_2w_m2_C9


title: RNA-Seq single cell_CKp25_2w_m2_C5


title: CD3/28_24h_1


title: RNA-Seq single cell_CKp25_2w_m2_C4


title: RNA-Seq single cell_CKp25_2w_m2_C3


title: CD3/28_3h_2

source_name: helper T cell_CD3/28_3h

value: anti-CD3/28 for 3hrs


title: RNA-Seq single cell_CKp25_2w_m2_D10


title: RNA-Seq single cell_CKp25_2w_m2_C6


title: Meteor KO Day 3 differentiated cells [3KOd3]

city: Lausanne

first: Daniel

last: Maric

state: Vaud

address: Rue du Bugnon 27

department: Coeur-vaisseaux

country: Switzerland

institute: CHUV

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus genome (v. GRCm38) using STAR (v. 2.4.2a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using M. musculus gene annotation (Ensembl v.82).
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: Meteor KO Day 3 differentiated cells

growth_protocol: Mouse embryonic EomesEGFP reporter stem cells (WT and KO) were cultured on mouse embryonic fibroblast feeders in standard ES cell medium

extract_protocol:
Total RNA was isolated using the RNeasy isolation kit (Qiagen).
Sequencing libraries were prepared according to Illumina TruSeq Stranded mRNA protocol instructions with PolyA selection. Libraries were sequenced with the Illumina HiSeq2500 (1x100 bp).
RNAseq. Sequencing data was generated and analyzed at the Lausanne Genomic Technologies Facility.

treatment_protocol: Cardiac differentiation of ES cells was induced by aggregating aliquots containing ~1000 cells in hanging drop of 25µl of differentiation medium: IMDM (Life Technologies #21980-032) medium supplemented with 200mM L-glutamine (Life Technologies #25030-024), 20% FBS, 6.5µl of 1-thioglycerol (Sigma #M6145), 1M L-ascorbic acid (Sigma #A4544) and Gentamicin (1:500) to form embryoid bodies.

tag: strain background

tag: genotype/variation

value: Meteor KO

value: Mouse Embryonic Stem Cells

tag: cell subtype

value: Day3 differentiated cells with deletion of Meteor enhancer


title: CD3/28+cGAMP_3h_2

source_name: helper T cell_CD3/28+cGAMP_3h

value: anti-CD3/28+cGAMP for 3hrs


title: Meteor KO Day 3 differentiated cells [2KOd3]


title: CD3/28+cGAMP_3h_1


title: Meteor KO Day 0 ESCs [2KOd0]

source_name: Meteor KO Day 0 ESCs

value: ESCs with deletion of Meteor enhancer


title: RNA-Seq single cell_CKp25_2w_m2_F9


title: Meteor KO Day 0 ESCs [3KOd0]


title: Naive CD4_2

source_name: helper T cell_Naive CD4

value: none (naïve)


title: RNA-Seq single cell_CKp25_2w_m2_C1


title: Meteor KO Day 0 ESCs [1KOd0]


title: Meteor KO Day 3 differentiated cells [1KOd3]


title: WT Day 3 differentiated cells [3wtd3]

source_name: WT Day 3 differentiated cells

value: Day3 differentiated cells


title: RNA-Seq single cell_CKp25_2w_m2_B12

value: isolated, FACS sorted single hippocampal microglia


title: RNA-Seq single cell_CKp25_2w_m2_B11


title: WT Day 3 differentiated cells [1wtd3]


title: Naive CD4_1


title: WT Day 0 ESCs [1wtd0]

source_name: WT Day 0 ESCs

value: Pluripotent ESCs


title: RNA-Seq single cell_CKp25_2w_m2_B10

value: 3 months and 2 weeks


title: WT Day 3 differentiated cells [2wtd3]


title: CD3/28_3h_1

value: spleen


title: INPUT_ChIPSeq Day3 Eomes pos. (DVM27)

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

institute: Swiss Institute of Bioinformatics

description:
DVM27
Processed data file: D3Pos_INPUT.bw

library_source: genomic

data_processing:
Reads were aligned using bowtie2 (2.2.4) with --non-deterministic option. The rest was default.
Duplicated reads have been removed using PICARD 1.80.
Bigwig tracks have been generated from the bam files using USEQ tool 8.9.3, pooling the replicates by condition.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

source_name: Mouse Embryonic Stem Cells

growth_protocol: Mouse embryonic EomesEGFP reporter stem cells were cultured on mouse embryonic fibroblast feeders in standard ES cell medium.

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries for sequencing were prepared with MicroPlex v2 kit (Diagenode) using 10ng of Chromatin without size selection from total input chromatin and immunoprecipitated DNA. Libraries were subjected to paired-end read analysis on an Illumina HiSeq 2500.

tag: strain/background

value: Differentiated cells sorted for Eomes (positive)

tag: chip antibody


title: INPUT_ChIPSeq Day3 Eomes neg. (DVM26)

description:
DVM26
Processed data file: D3neg_INPUT.bw

value: Differentiated cells sorted for Eomes (negative)


title: RNA-Seq single cell_CKp25_2w_m2_B8


title: H3K27Ac_ChIPSeq Day3 Eomes pos. (DVM24)

description:
DVM24
Processed data file: D3Pos_H3K27Ac.bw


title: RNA-Seq single cell_CKp25_2w_m2_B9


title: INPUT_ChIPseq ESC (DVM25)

description:
DVM25
Processed data file: D0_INPUT.bw

value: Pluripotent Stem Cells


title: H3K4me3_ChIPSeq Day3 Eomes pos. (DVM23)

description:
DVM23
Processed data file: D3Pos_H3K4me3.bw


title: RNA-Seq single cell_CKp25_2w_m2_B7


title: RNA-Seq single cell_CKp25_2w_m2_C2


title: H3K27Ac_ChIPSeq Day3 Eomes neg. (DVM22)

description:
DVM22
Processed data file: D3neg_H3K27Ac.bw


title: H3K4me3_ChIPSeq Day3 Eomes neg. (DVM21)

description:
DVM21
Processed data file: D3neg_H3K4me3.bw


title: RNA-Seq single cell_CKp25_2w_m2_B6


title: RNA-Seq single cell_CKp25_2w_m2_B5


title: H3K4me3_ChIPSeq ESC (DVM19)

description:
DVM19
Processed data file: D0_H3K4me3.bw


title: INPUT_ChIPSeq Day3 Eomes pos. (DVM18)

description:
DVM18
Processed data file: D3Pos_INPUT.bw


title: INPUT_ChIPseq ESC (DVM16)

description:
DVM16
Processed data file: D0_INPUT.bw


title: WT Day 0 ESCs [3wtd0]

value: wild type


title: H3K27Ac_ChIPSeq ESC (DVM20)

description:
DVM20
Processed data file: D0_H3K27Ac.bw


title: H3K4me3_ChIPSeq Day3 Eomes pos. (DVM14)

description:
DVM14
Processed data file: D3Pos_H3K4me3.bw


title: WT Day 0 ESCs [2wtd0]


title: H3K4me3_ChIPSeq Day3 Eomes neg. (DVM12)

description:
DVM12
Processed data file: D3neg_H3K4me3.bw


title: RNA-Seq single cell_CKp25_2w_m2_B3


title: RNA-Seq single cell_CKp25_2w_m2_B2


title: H3K4me3_ChIPSeq ESC (DVM10)

description:
DVM10
Processed data file: D0_H3K4me3.bw


title: INPUT_ChIPseq ESC (DVM07)

description:
DVM07
Processed data file: D0_INPUT.bw


title: RNA-Seq single cell_CKp25_2w_m2_B1


title: H3K4me3_ChIPSeq Day3 Eomes pos. (DVM05)

description:
DVM05
Processed data file: D3Pos_H3K4me3.bw


title: H3K27Ac_ChIPSeq Day3 Eomes neg. (DVM04)

description:
DVM04
Processed data file: D3neg_H3K27Ac.bw


title: RNA-Seq single cell_CKp25_2w_m2_A12


title: RNA-Seq single cell_CKp25_2w_m2_A11


title: H3K27Ac_ChIPSeq Day3 Eomes pos. (DVM06)

description:
DVM06
Processed data file: D3Pos_H3K27Ac.bw


title: RNA-Seq single cell_CKp25_2w_m2_A10


title: H3K4me3_ChIPSeq ESC (DVM01)

description:
DVM01
Processed data file: D0_H3K4me3.bw


title: H3K4me3_ChIPSeq Day3 Eomes neg. (DVM03)

description:
DVM03
Processed data file: D3neg_H3K4me3.bw


title: RNA-Seq single cell_CKp25_2w_m2_B4


title: INPUT_ChIPSeq Day3 Eomes neg. (DVM17)

description:
DVM17
Processed data file: D3neg_INPUT.bw


title: RNAseq Day3 Eomes pos. (6D3P)

description:
6D3P
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.90.
Sequences were aligned to mm10 reference genome using STAR 2.0.4.
Novel transcripts were predicted with Cufflinks 2.2.1.
Novel transcripts predictions were merged with mm10 reference genome using Cuffmerge 2.2.1 with option -G with mm10 reference GTF.
Counts were generated using htseq-count v0.6.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw_counts.txt.gz, normalized_counts_CPM.txt.gz: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package edgeR calcNormFactors and cpm function. Count data are provided in tab-delimited text format.

extract_protocol:
Total RNA was isolated using the RNeasy isolation kit (Qiagen).
Sequencing libraries were prepared according to Illumina RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq 2500 (2x100bp) using 2 lanes/sample with a multiplex level of 1 (approximately 5x10e8 reads per sample).


title: RNAseq Day3 Eomes pos. (2D3P)

description:
2D3P
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNAseq Day3 Eomes pos. (5D3P)

description:
5D3P
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNAseq Day3 Eomes neg. (6D3N)

description:
6D3N
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNA-Seq single cell_CKp25_2w_m2_A8


title: RNAseq Day3 Eomes neg. (5D3N)

description:
5D3N
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNAseq ESC (6D0)

description:
6D0
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNA-Seq single cell_CKp25_2w_m2_A7


title: INPUT_ChIPSeq Day3 Eomes neg. (DVM08)

description:
DVM08
Processed data file: D3neg_INPUT.bw


title: RNA-Seq single cell_CKp25_2w_m2_A6


title: RNAseq Day3 Eomes neg. (1D3N)

description:
1D3N
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: INPUT_ChIPSeq Day3 Eomes pos. (DVM09)

description:
DVM09
Processed data file: D3Pos_INPUT.bw


title: RNAseq ESC (5D0)

description:
5D0
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNAseq ESC (2D0)

description:
2D0
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNA-Seq single cell_CKp25_2w_m2_A4


title: RNA-Seq single cell_CKp25_2w_m2_A2


title: RNAseq ESC (1D0)

description:
1D0
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: ARCKO10 r2

city: Irvine

first: Andrea

middle: J.

last: Tenner

state: California

address: 3205 McGaugh Hall

institute: University of California, Irvine

data_processing:
Pair-end RNA-seq reads were aligned using STAR v.2.5.1b with parameters ‘--outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.1 --outFilterMultimapNmax 10’ to the reference genome GRCm38/mm10.
We used STAR to then convert to transcriptome-based mapping with gene annotation gencode M8. Gene expression was measured using RSEM v.1.2.25 with expression values normalized into transcripts per million  (TPM).
Libraries with uniquely mapping percentages higher than 65% were kept for downstream analysis. Protein coding and long non-coding RNA genes, with expression TPM >=0.5 in at least one duplicates were collected and quantile normalized for subsequent differential gene expression and pathway analysis.
Genome_build: mm10
Supplementary_files_format_and_content: count file: merge_pc_lncRNA_count.txt
Supplementary_files_format_and_content: gene expression tpm file: merge_pc_lncRNA_tpm.txt

source_name: microglia

growth_protocol: All animal experimental procedures were reviewed and approved by the Institutional Animal Care and Use Committee of University of California at Irvine, and performed in accordance with the NIH Guide for the Care and Use of Laboratory Animals. Homozygous breeding pairs of CX3CR1-GFP and CCR2-RFP mice were obtained from Jackson Laboratories and bred to C57/B6J produce double homozygous CX3CR1GFP/GFPCCR2RFP/RFP reporter mice. Double homozygous reporter mice were bred with Arc48 (Cheng et al., 2004) Arctic mutant hAPP mice (from Dr. Lennart Mucke, Gladstone Institute, San Francisco, CA, USA) to generate mice heterozygous for hAPP, CX3CR1GFP/+CCR2RFP/+APP+/- (Arctic). Littermates lacking hAPP were used as controls (WT). C5a receptor knockout mice generated by target deletion of the C5a receptor gene (Hollmann et al., 2008), and bred with CX3CR1GFP/GFPCCR2RFP/RFPAPP+/- mice to produce Arctic mice lacking C5a receptor1 (Arctic/C5aR1KO) and APP-/- mice lacking the C5a receptor (C5aR1KO).

extract_protocol:
Mice from WT, C5aR1KO, Arctic and Arctic/C5aR1KO genotypes were perfused with PBS at 2, 5, 7 and 10 mo, and the brains (without olfactory bulbs, cerebellum, or midbrain) collected for microglia isolation. Brains were treated with Dispase II (Roche) at 37˚C for 1 hr and passed through a 70 µM nylon cell mesh strainer (BD Biosciences) to obtain a single cell suspension. The cell suspension was washed in Hanks’ balanced salt solution (HBSS; ThermoFisher) and spun at 1000 x g for 10 min at 4˚C. The cell pellet was resuspended in 70% Percoll (Sigma; diluted in HBSS), and 35% Percoll (diluted in HBSS) was carefully layered over to create a discontinuous Percoll gradient.  After centrifugation at 800 x g for 45 min at 4˚C, the cells at the interphase were quickly collected, washed with HBSS + 2% FBS and passed through a 40 µM nylon mesh cell strainer. Using a FACS Aria II, the viable cell population from a propidium iodide stained control was gated based on forward and side scatter properties. Using these forward and side scatter parameters, the GFP+RFP+ and the GFP+RFP- cells were sorted and collected. Total RNA from and GFP+RFP- cells was extracted for library construction.
Total RNA from and GFP+RFP- cells was extracted using the Illustra RNAspin mini isolation kit (GE Healthcare). For qRT-PCR, RNA was converted to cDNA using Superscript III reverse transcriptase (Life Technologies) following manufacturer’s instructions. RNA was quantified using the NanoDrop ND-1000 spectrophotometer and the quality checked using the Agilent Bioanalyzer 2100. The SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Clonetech Laboratories) was used to generate Illumina-compatible RNA-seq libraries. Briefly, total RNA was converted into cDNA and then adapters with barcodes for Illumina sequencing were added by PCR.  The PCR products were then purified and the ribosomal cDNA depleted with sequence specific probes and RNaseH. The barcoded cDNA libraries were sequenced on the Illumina HiSeq 2500 platform to yield 100-bp paired-end reads.

value: Arctic C5aR1 knockout

value: microglia

value: 10-11 month


title: RNA-Seq single cell_CKp25_2w_m2_A9


title: ARCKO10 r1


title: ARCKO7 r1

value: 7 month


title: ARCKO5 r2

value: 5 month


title: ARCKO7 r2


title: RNA-Seq single cell_CKp25_2w_m2_A1


title: RNAseq Day3 Eomes pos. (1D3P)

description:
1D3P
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: RNA-Seq single cell_CK_2w_m2_H12

value: CK


title: RNAseq Day3 Eomes neg. (2D3N)

description:
2D3N
Processed data file: raw_counts.txt.gz
Processed data file: normalized_counts_CPM.txt.gz
Processed data file: transcripts.gtf.gz


title: ARCKO5 r1


title: ARCKO2 r1

value: 2 month


title: RNA-Seq single cell_CK_2w_m2_H11


title: ARCKO2 r2


title: RNA-Seq single cell_CKp25_2w_m2_A5


title: ARC10 r2

value: Arctic


title: ARC10 r1


title: RNA-Seq single cell_CK_2w_m2_H10


title: ARC7 r2


title: ARC5 r2


title: ARC7 r1


title: RNA-Seq single cell_CK_2w_m2_H9


title: ARC5 r1


title: RNA-Seq single cell_CKp25_2w_m2_A3


title: RNA-Seq single cell_CK_2w_m2_H8


title: RNA-Seq single cell_CK_2w_m2_H7


title: KO10 r1

value: C5aR1 knockout


title: RNA-Seq single cell_CK_2w_m2_H6

value: isolated, FACS sorted single hippocampal microglia


title: KO7 r2


title: RNA-Seq single cell_CK_2w_m2_H5


title: KO7 r1


title: KO5 r2


title: KO2 r2


title: KO5 r1


title: KO2 r1


title: RNA-Seq single cell_CK_2w_m2_H3


title: WT10 r2

value: Wildtype


title: WT7 r2


title: WT10 r1


title: ARC2 r2


title: WT7 r1


title: WT5 r2


title: RNA-Seq single cell_CK_2w_m2_H2

value: 3 months and 2 weeks


title: RNA-Seq single cell_CK_2w_m2_G12


title: WT2 r2


title: RNA-Seq single cell_CK_2w_m2_H1


title: WT5 r1


title: H3K27Ac_ChIPSeq ESC (DVM02)

description:
DVM02
Processed data file: D0_H3K27Ac.bw


title: WT2 r1


title: KO10 r2


title: ARC2 r1


title: RNA-Seq single cell_CK_2w_m2_G11


title: Pkp4_CB_4

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

data_processing:
Basecalling by RTA 1.18.64, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (STAR_2.4.2a) on 2-pass mode with mouse gencode (release 4) gtf
Genes were subsequently counted using Rsubread (v. 1.20.1) and analyzed for gene expression changes using limma-voom (limma, v. 3.26.1).

source_name: cell body-Pkp4-rep4

growth_protocol: NIH/3T3 cell lines grown in DMEM+10% calf serum

extract_protocol:
Total RNA from protrusion and cell body extracts was isolated using Trizol LS. The recovered RNA was treated with RQ1 DNase for 30min at 37C and isolated with Trizol LS (Invitrogen)
Libraries were constructed with Illumina stranded total RNA library prep kit (RS-122-2201)

treatment_protocol: Expression of beta-globin constructs was induced by addition of 1 microgr/ml doxycycline for 3 days. Protrusions and cell bodies were isolated from serum-starved cells plated for 2 hrs on Transwell inserts equipped with 3.0-μm porous polycarbonate membrane (Corning). LPA was added to the bottom chamber for 1 hr and the cells were fixed with 0.3% paraformaldehyde for 10 min. Protrusions and cell bodies were scraped in crosslink reversal buffer (100mM Tris pH 6.8, 5mM EDTA, 10mM DTT and 1% SDS) and the extracts were incubated for 45min at 70C.

tag: cell line

value: NIH/3T3 cells

tag: subcellular fraction

value: Cell body

tag: stably expressed construct

value: beta-globin coding sequence/Pkp4 UTR


title: Pkp4_Ps_3

value: Protrusions


title: Pkp4_CB_3

source_name: cell body-Pkp4-rep3


title: Pkp4_Ps_4


title: Pkp4_CB_2

source_name: cell body-Pkp4-rep2


title: RNA-Seq single cell_CK_2w_m2_G10


title: RNA-Seq single cell_CK_2w_m2_G9


title: RNA-Seq single cell_CK_2w_m2_G7


title: RNA-Seq single cell_CK_2w_m2_H4


title: Pkp4_Ps_1


title: Pkp4_CB_1

source_name: cell body-Pkp4-rep1


title: HBB_CB_4

source_name: cell body-HBB-rep4

value: beta-globin coding sequence/HBB UTR


title: HBB_CB_3

source_name: cell body-HBB-rep3


title: RNA-Seq single cell_CK_2w_m2_G6


title: HBB_Ps_3


title: RNA-Seq single cell_CK_2w_m2_G8


title: HBB_CB_1

source_name: cell body-HBB-rep1


title: RNA-Seq single cell_CK_2w_m2_G2


title: Con_Ps_1

growth_protocol: NIH/3T3 cells grown in DMEM+10% calf serum

treatment_protocol: Protrusions and cell bodies were isolated from serum-starved cells plated for 2 hrs on Transwell inserts equipped with 3.0-μm porous polycarbonate membrane (Corning). LPA was added to the bottom chamber for 1 hr and the cells were fixed with 0.3% paraformaldehyde for 10 min. Protrusions and cell bodies were scraped in crosslink reversal buffer (100mM Tris pH 6.8, 5mM EDTA, 10mM DTT and 1% SDS) and teh extracts were incubated for 45min at 70C.

tag: sirna trasnfection

value: control


title: HBB_Ps_4


title: HBB_Ps_2


title: Con_CB_4

source_name: cell body-siControl-rep4


title: RNA-Seq single cell_CK_2w_m2_G5


title: RNA-Seq single cell_CK_2w_m2_G4


title: HBB_Ps_1


title: Pkp4_Ps_2


title: Con_Ps_2


title: Con_CB_3

source_name: cell body-siControl-rep3


title: RNA-Seq single cell_CK_2w_m2_F12


title: RNA-Seq single cell_CK_2w_m2_G1


title: APC_Ps_4

value: APC


title: Con_CB_2

source_name: cell body-siControl-rep2


title: HBB_CB_2

source_name: cell body-HBB-rep2


title: Con_CB_1

source_name: cell body-siControl-rep1


title: APC_Ps_2


title: APC_CB_4

source_name: cell body-siAPC-rep4


title: RNA-Seq single cell_CK_2w_m2_F10


title: Con_Ps_4


title: APC_Ps_1


title: RNA-Seq single cell_CK_2w_m2_G3


title: RNA-Seq single cell_CK_2w_m2_F9


title: Con_Ps_3


title: APC_CB_2

source_name: cell body-siAPC-rep2


title: APC_CB_3

source_name: cell body-siAPC-rep3


title: RNA-Seq single cell_CK_2w_m2_F8


title: APC_CB_1

source_name: cell body-siAPC-rep1


title: RNA-Seq single cell_CK_2w_m2_F7


title: IAP-rep 2 methylgene

city: Hangzhou

first: Jian

last: zhang

state: Zhejiang

address: 28 shuidaosuo road,Fuyang, Hangzhou

department: State Key Lab of Rice Biology

country: China

institute: China National Rice Research Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rice whole genome using bismark software with parameters -Clean Reads -Unique mapped -Mapped(%) -Conversion_rate(%).
5mC detection and annotation were done by bismark_methylation_extractor.
Genome_build: Rice genome annotation project database(MSU7): (ftp://plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/)
Supplementary_files_format_and_content: txt files include Chromosome,ChromStart,ChromEnd,Name,Strand,IBP_J01,IBP_J02,IBP_J03,IBP_Mean,IAP_J04,IAP_J05,IAP_J06,IAP_Mean,Dependant_Tvalue,Fredom-degree,p-Value,FDR_by_Bonferroni values for each Sample …

organism: Oryza sativa

source_name: integument after pollination (IAP)

growth_protocol: Rice (Oryza sativa L. cv. Nipponbare) plants were grown in the field.To prevent contamination from pollinated pistils, the mature pistil was manually dissected with glumes and collected before the panicles fully headed out.

extract_protocol:
Genomic DNA of samples was extracted using a CTAB method.The DNA quality was evaluated by agarose gel electrophoresis and NANODROP spectrophotometer alalysis (Thermo, American).
The two different samples (integument before/after pollination, IBP/IAP) were sonicated to produce DNA fragmentation. After end repairing, 3' end A-tailing, ligating to bisulfite-converted adaptors, the purified DNA fragments ranging from 100 to 500 bp were treated with bisulfite containing a C-T conversion reagent under denaturing conditions. After that, following PCR amplification, qualified DNA sequencing libraries were generated and sequenced on the IlluminaHiSeqTM 2500 (Illumina, CA, USA) following the manufacturer’s instructions to generate paired-end 125-bp reads.

tag: cultivar

value: Nipponbare

value: integument after pollination (IAP)

value: wild type

value: early seed development


title: IAP-rep 3 methylgene


title: RNA-Seq single cell_CK_2w_m2_F5

value: CK


title: IBP-rep 3 methylgene

source_name: integument before pollination (IBP)

value: integument before pollination (IBP)


title: IAP-rep 1 methylgene


title: IBP-rep 2 methylgene


title: IBP-rep 1 methylgene


title: RNA-Seq single cell_CK_2w_m2_F11


title: RNA-Seq single cell_CK_2w_m2_F4


title: setB_PS_6_hr

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Dr MC 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Mapping of the RNA-Seq reads to human genome and transcriptome: Omicsoft sequence aligner (OSAv4.0.2.1) was used to map the reads (single-end sequencing) to human genome (version B37.3) and transcriptome (Refgene) using default parameters/options and ExpressionMeasurement=Count_Transcript, SearchNovelExonJunction=True. Average read count for the samples was 30-40 million and about 94% reads were uniquely mapped for all samples.
Genome_build: Human.B37.3 (based on NCBI build 37.3)
Supplementary_files_format_and_content: tab delimited text file, *.txt.gz. The first nine columns contain information on the Refseq (Refgene) transcripts (such as transcript/gene name). The remaining columns correspond to samples and contain the raw mapped read counts. SetA and SetB correspond to replicates 1 and 2, respectively.

molecule: polyA RNA

organism: Homo sapiens

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in medium M199 (Gibco) supplemented with 15% FBS (Omega), 3 ng/mL β-EC growth factor (Sigma), 4 U/mL heparin (Sigma), and 100 U/mL penicillin-streptomycin.

extract_protocol:
Samples for RNA sequencing analysis were collected at 1, 2, 3, 4, 6, 9, 12, 16, 20, and 24 hours after exposure to shear. Samples for RNA sequencing analysis were collected at hour 1 for the ST condition.
Total RNA were extracted by using the mirVana miRNA Isolation Kit (Ambion, Cat#AM1560). The RNAs were polyA selected, fragmented, and random hexamer primed using Illumina TruSeq stranded mRNA sample preparation kit. Constructed cDNA library was subjected to single-ended 50-bp sequencing on Illumina Hi-seq 2000 instrument.

treatment_protocol: Pulsatile shear ﬂow (PS) or oscillatory shear ﬂow (OS) was applied to ECs with a shear stress of 12 ± 5 dyn/cm2 or 0.5 ± 5 dyn/cm2, respectively. ECs were also exposed to a “low flow” condition, i.e. 0.5 dyn/cm2 laminar flow, and designated as a “static” flow condition (ST).

value: Blood vessel

value: HUVEC

tag: condition

value: PS


title: setB_PS_4_hr


title: RNA-Seq single cell_CK_2w_m2_F3

tag: strain

value: 3 months and 2 weeks

value: isolated, FACS sorted single hippocampal microglia


title: RNA-Seq single cell_CK_2w_m2_F2

tag: age


title: setB_PS_3_hr

tag: cell type


title: setB_PS_24_hr

tag: tissue


title: setB_PS_9_hr


title: setB_PS_2_hr


title: RNA-Seq single cell_CK_2w_m2_F1


title: setB_PS_16_hr


title: RNA-Seq single cell_CK_2w_m2_E12


title: setB_PS_12_hr


title: setB_PS_1_hr


title: RNA-Seq single cell_CK_2w_m2_E11


title: APC_Ps_3

value: NIH/3T3 cells


title: setB_OS_9_hr

value: OS


title: setB_OS_6_hr


title: RNA-Seq single cell_CK_2w_m2_E10


title: RNA-Seq single cell_CK_2w_m2_F6


title: setB_OS_4_hr


title: RNA-Seq single cell_CK_2w_m2_E8


title: RNA-Seq single cell_CK_2w_m2_E7


title: setB_OS_3_hr


title: setB_OS_2_hr


title: RNAseq Bex1 2 -19

city: Cincinnati

first: Tobias

last: Schips

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
bex1 replicate 2
Federica-19

data_processing:
Sequence reads were aligned to the reference genome by using the TopHat aligner, and reads aligning to each known transcript were counted by using Bioconductor packages for next-generation sequencing data analysis.
P-values were calculated using a negative binomial statistical model as implemented in DESeq [Bioconductor version: Release (2.14)], meanwhile false discover rates were used to obtain the adjusted P-values.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: Microsoft Excel xlsx and differential gene expression

organism: Rattus norvegicus

source_name: neonatale rat cardiomyocytes

growth_protocol: Neonatale rat cardiomyocytes were isolated from 1-3 day old rat pubs. Cells were infected with Bex1 or beta galactosidase adenovirus and cultured for 48h in M199 Medium with 2% serum.

extract_protocol:
RNA was isolated using the RNeasy kit according to manufacturer’s instructions (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: virus

value: neonatale rat cardiomyocytes


title: RNAseq Bex1 1 -18

description:
bex1 replicate 1
Federica-18


title: RNA-Seq single cell_CK_2w_m2_E6


title: setB_PS_20_hr


title: RNAseq Control 2 -17

description:
control replicate 2
Federica-17

value: beta galactosidase


title: setB_OS_24_hr


title: RNAseq Control 1 -16

description:
control replicate 1
Federica-16


title: RNA-Seq single cell_CK_2w_m2_E5


title: RIPseq Bex1 FE

growth_protocol: Neonatale rat cardiomyocytes were isolated from 1-3 day old rat pubs. Cells were infected with Bex1-flag or beta galactosidase adenovirus and cultured for 48h in M199 Medium with 2% serum.

extract_protocol:
Magna RIP kit (Millipore) was used to performed RNA immunoprecipitation from neonatal rat cardiomyocyte. Anti-Flag M2 magnetic beads (M8823, Sigma) were used for standard pull down of the ribonucleoprotein complex. For RIP-sequencing, RNA from 3 independent experiments was pulled into each sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ip antibody

value: Flag M2 sigma


title: setB_OS_20_hr


title: RIPseq Control FC

description: control


title: RNA-Seq single cell_CK_2w_m2_E3


title: setB_OS_1_hr


title: RNA-Seq single cell_CK_2w_m2_E9


title: setB_OS_12_hr


title: RNA-Seq single cell_CK_2w_m2_E1


title: RNA-Seq single cell_CK_2w_m2_E4


title: RNA-Seq single cell_CK_2w_m2_E2


title: ZZ3

city: New York

first: Sofie

last: Delbare

state: NY

address: 435 East 30th Street

institute: NYU Langone

description: adapter removed from reads in fastq file

data_processing:
FastQC (http://www.bioinformatics. bbsrc.ac.uk/projects/fastqc): used to assess quality of libraries.
Trimmomatic: Bases at the 5’ end of reads with a phred score lower than 20 were removed. Reads shorter than 32 bp were discarded. (Parameters: -phred 33; TRAILING:20; MINLEN:32)
Tophat2 was used to align reads to the reference genome. We used the default settings and did not include novel splice discovery, similar to Trapnell et al. (2012).
HTseq-count (Anders et al., 2015) was used to determine the raw number of read counts per gene.
Genome_build: dm3
Supplementary_files_format_and_content: HTSeq_raw_read_counts.txt contains the raw read counts for all samples (except sample IZ2). Read counts were determined using HTSeq-count (Anders et al. 2015)

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Flies were maintained on standard yeast/glucose media on a 12h light/ dark cycle at 25° C. Virgin females and males were aged 3-5 days in single-sex groups before the start of each experiment.

extract_protocol:
RNA was extracted from whole flies using Trizol (Rio et al., 2010). Five to ten females were pooled per replicate
RNAseq libraries were prepared using Illumina’s Truseq RNA Library Preparation Kit v2 (cat# RS-122-2001, RS-122-2002). Samples were sequenced in a single-end 100 bp run on a HiSeq2000, at the Genomics Facility in the Cornell Biotechnology Resource Center.

treatment_protocol: Virgin females from each line were singly-mated to virgin males from each of the five inbred lines, similar to a 5x5 full factorial design. For RNAseq, mated females were flash frozen 5 to 6h after the start of mating. Age-matched virgin females were flash-frozen in parallel.

tag: female genotype

value: Zimbabwe

tag: genotype of male the female mated with

tag: replicate


title: setB_low_flow_1_hr

value: ST


title: setB_OS_16_hr


title: RNA-Seq single cell_CK_2w_m2_D12


title: ZZ2


title: RNA-Seq single cell_CK_2w_m2_D10


title: setA_PS_6_hr


title: ZZ1


title: setA_PS_9_hr


title: ZT3

value: Tasmania


title: setA_PS_4_hr


title: RNA-Seq single cell_CK_2w_m2_D9


title: RNA-Seq single cell_CK_2w_m2_D11


title: ZT1


title: ZT2


title: RNA-Seq single cell_CK_2w_m2_D8


title: ZN3

value: Netherlands


title: setA_PS_3_hr


title: RNA-Seq single cell_CK_2w_m2_D6


title: setA_PS_2_hr


title: setA_PS_20_hr


title: setA_PS_24_hr


title: ZN2


title: setA_PS_1_hr


title: RNA-Seq single cell_CK_2w_m2_D5


title: ZN1


title: RNA-Seq single cell_CK_2w_m2_D4


title: ZI3

value: Ithaca


title: ZI1


title: setA_PS_16_hr


title: setA_PS_12_hr


title: ZB3

value: Beijing


title: RNA-Seq single cell_CK_2w_m2_D2

value: CK


title: ZI2


title: RNA-Seq single cell_CK_2w_m2_D1


title: RNA-Seq single cell_CK_2w_m2_D3


title: setA_OS_6_hr

value: Blood vessel


title: ZB2


title: setA_OS_9_hr

value: HUVEC


title: RNA-Seq single cell_CK_2w_m2_C12


title: RNA-Seq single cell_CK_2w_m2_D7


title: ZB1


title: setA_OS_4_hr


title: ZV3

value: virgin female


title: RNA-Seq single cell_CK_2w_m2_C10

value: 3 months and 2 weeks


title: RNA-Seq single cell_CK_2w_m2_C11

value: isolated, FACS sorted single hippocampal microglia


title: ZV2


title: setA_OS_2_hr


title: RNA-Seq single cell_CK_2w_m2_C8


title: setA_OS_24_hr


title: ZV1


title: RNA-Seq single cell_CK_2w_m2_C7


title: setA_OS_20_hr


title: RNA-Seq single cell_CK_2w_m2_C9


title: TZ3


title: TZ2


title: RNA-Seq single cell_CK_2w_m2_C6


title: setA_OS_16_hr


title: TZ1


title: setA_OS_1_hr


title: setA_OS_12_hr


title: RNA-Seq single cell_CK_2w_m2_C5


title: TT3


title: RNA-Seq single cell_CK_2w_m2_C3


title: setA_OS_3_hr


title: TT1


title: RNA-Seq single cell_CK_2w_m2_C2


title: TT2


title: setA_low_flow_1_hr


title: RNA-Seq single cell_CK_2w_m2_C4


title: RNA-Seq single cell_CK_2w_m2_C1


title: TN3


title: TN2


title: RNA-Seq single cell_CK_2w_m2_B12


title: H69 TEAD

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads for YAP, YAP  second run, YAP Santa Cruz, TEAD1 and Flag-Bio-YAP5SA have been used for peak-calling procedures using MACS software (version 1.3.7.1). A lower enrichment cutoff of 5 (mfold=5) has been set.
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for YAP, YAP Santa Cruz and TEAD1. Input signal has been used as background for YAP second run. BirA has been used as background for Flag-Bio-YAP5SA
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS

source_name: H69 human cell line

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size. Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen)
Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's reccomendations

value: TEAD


title: H69 YAP Santa Cruz

value: YAP Santa Cruz


title: TN1


title: H69 IgG

value: IgG


title: RNA-Seq single cell_CK_2w_m2_B11


title: TI3


title: RNA-Seq single cell_CK_2w_m2_B8


title: RNA-Seq single cell_CK_2w_m2_B9


title: TI2


title: TI1


title: TB3


title: RNA-Seq single cell_CK_2w_m2_B7


title: RNA-Seq single cell_CK_2w_m2_B6


title: RNA-Seq single cell_CK_2w_m2_B5


title: H69 YAP

value: YAP


title: TB2


title: RNA-Seq single cell_CK_2w_m2_B4


title: TV2


title: RNA-Seq single cell_CK_2w_m2_B3


title: TV3


title: NZ2


title: RNA-Seq single cell_CK_2w_m2_B2


title: TV1


title: RNA-Seq single cell_CK_2w_m2_B1


title: NZ3


title: RNA-Seq single cell_CK_2w_m2_A11


title: RNA-Seq single cell_CK_2w_m2_A12


title: RNA-Seq single cell_CK_2w_m2_B10


title: NT2


title: NT3


title: RNA-Seq single cell_CK_2w_m2_A10


title: RNA-Seq single cell_CK_2w_m2_A9


title: RNA-Seq single cell_CK_2w_m2_A7


title: NN3


title: NT1


title: TB1


title: NN2


title: RNA-Seq single cell_CK_2w_m2_A6


title: NN1


title: RNA-Seq single cell_CK_2w_m2_A5


title: NI3


title: RNA-Seq single cell_CK_2w_m2_A3


title: NI2


title: NB3


title: RNA-Seq single cell_CK_2w_m2_A2


title: RNA-Seq single cell_CK_2w_m2_A1


title: NI1


title: NZ1


title: NB2


title: NV3


title: NB1


title: H3K27ac IL-6 (rep#2)

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1126

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
ChIP-seq binding sites were identified as hotspots after adjustment using the input DNA control.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph

source_name: primary mouse hepatocytes

growth_protocol: mice maintained according to NIH guidelines under 12-hr light-dark cycles (light on at 6:00AM). Hepatocytes isolated by the two-step collagenase perfusion technique and treated the next day

extract_protocol:
crosslinked material was lyzed and sonicated. Chromatin precipitated with antibody and DNA was purified by ethanol precipitation
sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 50 bp single-end sequencing on Illumina HiSeq2000.

treatment_protocol: Hepatocytes treated with IL-1b (10ng/ml), IL-6 (10ng/ml) for 2 h.

value: primary hepatocytes


title: RNA-Seq single cell_CK_2w_m2_A8


title: H3K27ac dual (rep#1)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1148


title: H3K27ac dual (rep#2)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1127


title: IgG_ChIP

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

data_processing:
For ChIP- and DIP-seq, raw reads were trimmed to remove adapters using Trim Galore (v0.3.5) and Bowtie (v0.12.8) was used to obtain reads mapped uniquely to mouse genome (mm9).
The parameters used in Bowtie were ‘‘-v 3 -m 1 -y –best –strata’’. To accurately identify regions enriched for each cytosine modification, we first identified peak candidates with MACS (v2.1.1) (Ref. 31) using input as the control data set and using the following parameters:  [–bw 300 -m 5,30–shiftsize 100 -p 1e-3–slocal = 1000 -B–keep-dup = 1].
To remove nonspecific signals, IgG samples were processed similarly and their normalized read density (reads per kilobase per million) values were subtracted from modification-specific   peaks. The empirical FDR was estimated by exchanging the DIP and IgG control samples and identifying peaks in the control sample using the same set of parameters used for the DIP sample.
Called peaks were annotated with Gencode M1 and Cistrome CEAS32. Normalized read density plots centered on annotated elements downloaded from ENCODE were generated using NGSPLOT33. Peak overlap statistics were calculated using Fisherbed. All GO term analysis used DAVID (http://david.abcc.ncifcrf.gov).
For RRBS, adapter trimming for raw sequencing reads was performed using Trim Galore   and reads with a Phred score of less than 20 were excluded. Trimmed reads were mapped against the reference mouse genome (mm10) with Bismark (v0.14.5)
CpGs with a minimal coverage of 8 were included in further analysis steps. A Chi-square test was used to identify significant differentially methylated regions in KO vs wild-type samples, and an FDR-adjusted P <0.01 was used to determine DMRs.
Genome_build: mm9
Supplementary_files_format_and_content: bed files showing chromosomal coordinates for alinged reads of IgG ChIP control sample

source_name: mouse ES cells

growth_protocol: Co-derived wild-type and Srap1 KO mouse ES cells were cultured on gelatin-coated plates in high-glucose DMEM containing 15% FBS, 1x non-essential amino acids, 2 mM L-glutamine, 100 mM beta-mercaptoethanol, 1x nucleosides (Millipore), 1000U/ml leukemia inhibitory factor (StemRD) and 2i (selective GSK3β & Mek 1/2 inhibitors; Millipore), 25 mg/ml L-ascorbic acid.

extract_protocol:
For ChIP, mouse ES cells (C57BL/6N x 129/Sv background) stably expressing FHA-Srap1 were fixed in 1% paraformaldehyde for 10 min at 37 °C, followed by quenching with 125 mM glycine for 5 min. Cells were lysed and processed using the MAGnify ChIP system (Life Sciences). Lysates were sonicated using an ultrasonic processor (Cole Parmer) at power setting 3 in 30 s pulses followed by 1 min on ice, for a total of 6 min sonication.
Nucleoprotein complexes were immunoprecipitated using a mixture of M2 Flag and HA antisera (2.5 mg each) or equivalent amounts of isotype-matched mouse IgG per sample.
For DIP experiments, genomic DNA was isolated from Srap1 KO and matched wild-type ES cells using the DNeasy Blood & Tissue DNA kit and sonicated for a total of 6 min.
Samples were processed using the MeDIP or hMeDIP kits (Active Motif) according to the manufacturer’s protocol. For 5fC/5caC DIP, the hMeDIP protocol was followed using polyclonal antibodies to 5fC or 5caC.
Library preparation was performed using the Kapa HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase. Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on the Illumina HiSeq2000 or NextSeq500 for single-end reads.

value: cultured mouse ES cells

tag: passages

value: passages 3-5

value: mouse IgG1 (Invitrogen, 10005292, lot V017)

tag: molecule subtype

value: crosslinked cell lysate


title: NV1

value: Netherlands


title: IZ3

value: Ithaca

value: Zimbabwe


title: IZ2


title: H3K27ac IL-6 (rep#1)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1147


title: H3K27ac IL-1 (rep#1)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1145


title: RNA-Seq single cell_CK_2w_m2_A4

value: CK


title: H3K27ac NT (rep#2) control

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1123


title: H3K27ac NT (rep#1) control

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1144


title: IT3

value: Tasmania


title: IT2


title: RNA TNFa + IL-6  (rep#2)

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to mm9 using Casava Eland extended
Transcript levels were quantified using Tophat and Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was isolated using NucleoSpin kit (Macherey-Nagel).
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 200 bp paired-end sequencing on Illumina HiSeq2000.

treatment_protocol: Hepatocytes treated with IL-1b (10ng/ml), TNFa (2ng/ml), IL-6 (10ng/ml) for 2 h.


title: IT1


title: RNA TNFa + IL-6 (rep#1)


title: IN2


title: IN3


title: RNA IL-1 + IL-6 (rep#1)


title: IN1


title: RNA IL-6 (rep#2)


title: NV2

value: virgin female


title: II3


title: H3K27ac IL-1 (rep#2)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH1124


title: RNA IL-6 (rep#1)


title: II2


title: input GH2046

description:
chip antibody: n/a
GH2046


title: RNA TNFa (rep#2)


title: II1


title: STAT3 dual + DN-NFkB

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2648


title: STAT3 IL-6 + DN-NFkB

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2647


title: IB3

value: Beijing


title: IZ1


title: RNA TNFa (rep#1)


title: RNA IL-1 (rep#2)


title: RNA IL-1 (rep#1)


title: STAT3 NT + DN-NFkB

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2645


title: H3K27ac dual + DN-NFkB

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2644


title: RNA IL-1 + IL-6  (rep#2)


title: IB2


title: RNA NT (rep#2) control


title: IV3


title: H3K27ac IL-1 + DN-NFkB

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2642


title: IV1


title: H3K27ac NT + DN-NFkB

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2641


title: RRBS_Srap1_KO

data_processing:
For RRBS, adapter trimming for raw sequencing reads was performed using Trim Galore  and reads with a Phred score of less than 20 were excluded. Trimmed reads were mapped against the reference mouse genome (mm10) with Bismark (v0.14.5)
CpGs with a minimal coverage of 8 were included in further analysis steps. A Chi-square test was used to identify significant differentially methylated regions in KO vs wild-type samples, and an FDR-adjusted P <0.01 was used to determine DMRs.
Genome_build: mm10

source_name: E9.5 embryos

extract_protocol:
Genomic DNA was extracted from E9.5 wild-type and Srap1 KO embryos using the DNeasy Blood and Tissue kit (Qiagen) and digested with MspI overnight.
Size-selected (<0.7 kb) DNA fragments were subjected to library preparation using the Kapa HyperPrep kit (Kapa Biosystems) with methylated indexed primers (Illumina).
Bisulphite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research), followed by 12 cycles of PCR amplification using Kapa HiFi HotStart Uracil+ polymerase.
Amplified libraries were purified with 0.9X Ampure XP beads (BeckmanCoulter), then pooled and analyzed on the Illumina HiSeq2000 for 100 bp paired-end reads.
Library preparation was performed using the Kapa HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase. Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on the Illumina HiSeq2000 or NextSeq500 for single-end reads.

tag: strain background

tag: genotype/variation

value: Srap1 KO

tag: developmental stage

value: E9.5 embryos

value: MspI-digested, bisulfite converted genomic DNA


title: RNA NT (rep#1) control


title: BZ3


title: RRBS_WT

value: wild type


title: IV2


title: Srap1 KO_ mouse ES_RNA-seq

data_processing:
For RNA-seq, ChIP-seq and DIP-seq, raw reads were trimmed to remove adapters and low-quality reads using Trim Galore (v0.3.5).
Bowtie (v0.12.8) was used to obtain reads mapped uniquely to the mouse genome (mm9). ChIP and DIP peak candidates were identified with MACS (v2.1.1)using input as the control data set.
To remove nonspecific signals, IgG samples were processed similarly and their normalized read density (RPKM) values were subtracted from modification-specific peaks.
For RNA-seq, Cufflinks (v 2.2.1.0) was used to assemble transcripts, estimate their abundances and test for differential transcript expression.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Srap1 KO_mouse ES cells

extract_protocol:
For RNA-seq, total RNA was extracted from wild-type and Srap1 KO mouse ES cells using the Zymo RNA Clean & Concentrator (Zymo Research), followed by rRNA depletion and cDNA preparation using the KAPA Stranded RNA-Seq Kit with RiboErase.
Library preparations were performed using the Kapa HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase.
Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on the Illumina HiSeq2000 or NextSeq500.

value: embryonic stem cells (ES cells)

value: rRNA-depleted RNA


title: cJun IL-1

description:
chip antibody: cJun, CST, 60A8 #9165
GH2197

value: primary hepatocytes


title: BZ1


title: BZ2


title: IB1


title: STAT3 IL-1 + DN-NFkB

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2646


title: IgG_KO MeDIP-seq

data_processing:
For ChIP- and DIP-seq, raw reads were trimmed to remove adapters using Trim Galore (v0.3.5) and Bowtie (v0.12.8) was used to obtain reads mapped uniquely to mouse genome (mm9).
The parameters used in Bowtie were ‘‘-v 3 -m 1 -y –best –strata’’. To accurately identify regions enriched for each cytosine modification, we first identified peak candidates with MACS (v2.1.1) (Ref. 31) using input as the control data set and using the following parameters:  [–bw 300 -m 5,30–shiftsize 100 -p 1e-3–slocal = 1000 -B–keep-dup = 1].
To remove nonspecific signals, IgG samples were processed similarly and their normalized read density (reads per kilobase per million) values were subtracted from modification-specific   peaks. The empirical FDR was estimated by exchanging the DIP and IgG control samples and identifying peaks in the control sample using the same set of parameters used for the DIP sample.
Called peaks were annotated with Gencode M1 and Cistrome CEAS32. Normalized read density plots centered on annotated elements downloaded from ENCODE were generated using NGSPLOT33. Peak overlap statistics were calculated using Fisherbed. All GO term analysis used DAVID (http://david.abcc.ncifcrf.gov).
For RRBS, adapter trimming for raw sequencing reads was performed using Trim Galore   and reads with a Phred score of less than 20 were excluded. Trimmed reads were mapped against the reference mouse genome (mm10) with Bismark (v0.14.5)
CpGs with a minimal coverage of 8 were included in further analysis steps. A Chi-square test was used to identify significant differentially methylated regions in KO vs wild-type samples, and an FDR-adjusted P <0.01 was used to determine DMRs.
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using

value: cultured embryonic stem cells (ES cells)

value: passages 3-5

tag: antibody

value: control IgG


title: BT2

description: adapter removed from reads in fastq file


title: 5hmC_KO MeDIP-seq

value: 5-Hydroxymethylcytosine (5-hmC) antibody (pAb); Active Motif Cat. #39791


title: BT3


title: H3K27ac IL-6 + DN-NFkB

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2643


title: 5fC_WT MeDIP-seq

value: 5-Formylcytosine (5-fC) antibody (pAb); Active Motif Cat. #61227


title: p65 IL-1

description:
chip antibody: p65 Santa Croz cat# sc-372X
GH2651


title: BT1


title: 5fC_KO MeDIP-seq


title: STAT3 dual (rep#2)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2478


title: STAT3 dual (rep#1)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2474


title: STAT3 IL-6 (rep#2)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2477


title: BN3

value: Netherlands


title: 5mc_WT MeDIP-seq

value: 5-Methylcytosine (5-mC) antibody (pAb); Active Motif Cat. #61255


title: BN2


title: CEBPB IL-1

description:
chip antibody: CEBPB Santa Croz cat# sc-150X
GH2100


title: STAT3 IL-1 (rep#2)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2476


title: BN1


title: 5mc_KO MeDIP-seq


title: 5hmC_WT MeDIP-seq


title: STAT3 NT (rep#2)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2475


title: 5caC_KO MeDIP-seq

value: 5-Carboxylcytosine (5-caC) antibody; Active Motif Cat. #61229


title: 5caC_WT MeDIP-seq


title: BI3

value: Ithaca


title: BI1

value: Beijing


title: BB3


title: STAT3 NT (rep#1)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2471


title: RNA-Pol2 dual (rep#2)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2375


title: RNA-Pol2 IL-6 (rep#2)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2374


title: RNA-Pol2 IL-6 (rep#1)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2366


title: RNA-Pol2 dual (rep#1)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2367


title: RNA-Pol2 IL-1 (rep#2)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2373


title: BB2


title: BV3

value: virgin female


title: STAT3 IL-6 (rep#1)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2473


title: BV2


title: BV1


title: RNA-Pol2 IL-1 (rep#1)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2365


title: STAT3 IL-1 (rep#1)

description:
chip antibody: STAT3, Santa Croz cat# sc-482X
GH2472


title: RNA-Pol2 NT (rep#2)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2372


title: RNA-Pol2 NT (rep#1)

description:
chip antibody: RNA-Pol2, Abcam, cat# ab5131
GH2364


title: DMSO_12hr_DMSO_4hr_2

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
RNA-seq reads were aligned to a version of the hg19 human reference genome with ERCC spike-in reference sequences added using tophat (Trapnell et al., 2009) v.2.0.13 with parameters –nonovel-juncs and –G set to the human RefSeq transcript list downloaded in May 2013
Tophat-aligned BAM files were used to calculate expression values per transcript using RPKM_count.py from RSeQC. Transcript-level expression was extracted from the RPKM_count.py output.
Genome_build: hg19
Supplementary_files_format_and_content: RPKMtable files represent read counts and normalized read counts of RefSeq transcripts. Column 1-3 is the location of the ORF of the transcript named in Column 4. The gene strandedness is in Column 5. Column 6 and 7 are the raw and RPKM-normalized read counts in the exons of these genes. Column 8 is the common gene name.

growth_protocol: HCT-116 cells were grown in McCoy's 5A medium containing 10% fetal bovine serum and 1% penicillin-streptomycin under 5% CO2 at 37°C.  Cells were treated at 70-75% confluence with medium containing DMSO or 5-FU (40 μM) for 12 hr, washed twice with phosphate buffered saline (1X) and treated for 4 hr with medium containing DMSO or 2.5 μM 3-MB-PP1.

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen 74104).
Ribo-Zero kit was used for preparation of libraries, followed by single-end sequencing

treatment_protocol: HCT116 cells were treated with medium containing DMSO or 5-FU (40 μM) for 12 hr, washed twice with phosphate buffered saline (1X) and treated for 4 hr with medium containing DMSO or 2.5 μM 3-MB-PP1

tag: cell line

value: Colorectal cancer cell line

tag: treated with

value: DMSO for 12 hours followed by DMSO for 4 hours


title: DMSO_12hr_3MB_4hr_2

value: DMSO for 12 hours followed by 3-MB-PP1 for 4 hours


title: H3K27ac IL-6 (rep#3)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2202

tag: strain


title: DMSO_12hr_DMSO_4hr_1


title: FHA-Srap1 ChIP-Seq

value: stably expressing FHA-Srap1

tag: chip antibody

value: Flag (Sigma M2); HA tag (F-7), Santa Cruz Biotechnologies, sc-7392


title: H3K27ac dual (rep#3)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2203

value: primary hepatocytes


title: 5FU_12hr_DMSO_4hr_2

tag: cell type

value: 5-fluorouracil for 12 hours followed by DMSO for 4 hours


title: H3K27ac IL-1 (rep#3)

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2201

tag: tissue


title: DMSO_12hr_3MB_4hr_1


title: BI2

description: adapter removed from reads in fastq file


title: H3K27ac NT (rep#3) control

description:
chip antibody: H3K27ac, Active Motif cat# 39133
GH2200


title: 5FU_12hr_DMSO_4hr_1


title: 5FU_12hr_3MB_4hr_2

value: 5-fluorouracil for 12 hours followed by 3-MB-PP1 for 4 hours


title: HBMEC

city: Madison

first: Tongcheng

last: Qian

state: WI

address: 1415 Engineering Drive, Room 3745

institute: UW-Madison

data_processing:
Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
the RefSeq transcript levels (FPKMs) were quantified using the python script rpkmforgenes.py
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: primary human Brain Microvascular Endothelial Cells

growth_protocol: hPSC-derived brain microvascular endothelial cells at day 8 were maintained in hESFM supplied with B27 plus retinoic acid (10 µM)and bFGF (20ng/ml) from day 8 to day 9 and hESFM supplied with B27 from day 9 to day 10

extract_protocol:
RNA of hPSC-derived and primary brain microvascular endothelial cells were harvested using Trizol reagent. NuGEN Ovation RNA Library Prep was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard NuGEN protocols

value: Brain

value: human adult


title: 5caC_WT_2 MeDIP-seq

value: wild type

value: cultured mouse ES cells

value: passages 3-5


title: D-BMEC2

source_name: hPSC-derived Brain Microvascular Endothelial Cells

value: day 10 from hPSC


title: 5hmC_WT_2 MeDIP-seq

value: 5-Hydroxymethylcytosine (5-hmC) antibody (pAb); Active Motif Cat. #39791


title: 5caC_KO_2 MeDIP-seq

value: Srap1 KO

value: 5-Carboxylcytosine (5-caC) antibody; Active Motif Cat. #61229


title: 5fC_WT_2 MeDIP-seq

value: 5-Formylcytosine (5-fC) antibody (pAb); Active Motif Cat. #61227


title: FHA-Srap1_R2_ChIP-seq

value: M2 Flag + HA mAb


title: 5hmC_KO_2 MeDIP-seq


title: 5mC_KO_2 MeDIP-seq

value: 5-Methylcytosine (5-mC) antibody (pAb); Active Motif Cat. #61255


title: D-BMEC3


title: D-BMEC1


title: 5mC_WT_2 MeDIP-seq


title: MRS773

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

country: Germany

institute: Max Planck Institute For Molecular Genetics

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were mapped to hg19/GRCh37 whole genome using STAR aligner v 2.4.2a with double pass alignment. First mapping was obtained using Ensembl v73 coordinates as a framework, while the second mapping added splice sites which were found in the first pass.
Gene-read coverages were obtained using STAR aligners “--quantMode GeneCounts” option
Raw counts were processed in R using functions of the edgeR library to normalize (calcNormFactors), and calculate logratios and significance using a robust trended dispersion estimate. Counts per Million were calculated using the function cpm from edgeR
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: tab-delimited text file including raw counts and CPM values for each sample as well as the logratios and pValues calculated compairing all Campylobacter-infected vs all healthy samples

source_name: colon mucosa, colorectal biopsy

extract_protocol:
Biopsies were immediately frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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: sigmoid colon

tag: campylobacter-infected

value: no

tag: enteritis


title: MRS771


title: MRS770

value: yes


title: MRS767


title: MRS769


title: WT_mouse ES_RNA-seq 3

source_name: WT_mouse ES cells

value: embryonic stem cells (ES cells)

value: rRNA-depleted RNA


title: WT_mouse ES_RNA-seq 2


title: WT_mouse ES_RNA-seq 4


title: 5fC_KO_2 MeDIP-seq


title: WT_mouse ES_RNA-seq 1


title: 5FU_12hr_3MB_4hr_1

value: Colorectal cancer cell line

value: 5-fluorouracil for 12 hours followed by 3-MB-PP1 for 4 hours


title: IgG WT MeDIP-seq

value: cultured embryonic stem cells (ES cells)

value: wild type

value: control IgG


title: UM-BMEC

value: Brain

value: day 10 from hPSC


title: MRS766


title: input_KO MeDIP-seq

value: Srap1 KO

value: passages 3-5

value: none (input)


title: F613-1

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

data_processing:
Basecalling were performed by Illumina GA Pipeline v1.5
raw reads were filtered to generate clean data
clean reads were aligned against genome by  SOAP aligner/SOAP2（Li， 2009）
Reads per kilobase transcriptome per million mapped reads(RPKM) was used to analyze the expression of genes
Genome_build: Reference Genome Sequence is NZ_CM001015.1,NZ_CM001016.1,NZ_CM001017.1,NZ_CM001018.1,NZ_CM001019.1.
Supplementary_files_format_and_content: text files include RPKM values for each Sample .

organism: Streptomyces clavuligerus

source_name: mycelium

growth_protocol: the total RNA of S. clavuligerusF613-1 and ATCC27064 was extracted from cultures incubated at 30ºC for 72 h on liquid fermentation medium.

extract_protocol:
the mycelia were collected at 72 h, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA
The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).

tag: phenotype

value: industrial strain


title: MRS765


title: ATCC27064

value: wildtype


title: MRS774

value: sigmoid colon


title: SpM_ND_rep3

status: Public on Oct 09 2017

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

data_processing:
Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR .Mapped data were analyzed with HOMER's "analyzeRepeats" function with -noadj. To normalize for genomic DNA contamination, which occurred in some samples due to incomplete DNA removal during RNA isolation, the average intronic noise per base pair in all intronic regions per gene was calculated. The exonic reads were then normalized by subtracting the background noise per base pair for the complete length of the exonic regions. Genes without introns were not normalized, as these genes are the minority of genes and are typically short. After removal of contamination, gene isoforms were condensed and RPKM values were calculated.
Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR .Mapped data were analyzed with HOMER's "analyzeRepeats" function with -noadj. To normalize for genomic DNA contamination, which occurred in some samples due to incomplete DNA removal during RNA isolation, the average intronic noise per base pair in all intronic regions per gene was calculated. The exonic reads were then normalized by subtracting the background noise per base pair for the complete length of the exonic regions. Genes without introns were not normalized, as these genes are the minority of genes and are typically short. After removal of contamination, gene isoforms were condensed and RPKM values were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for low input RNA-seq, table of unnormalized read counts for low input RNA-Seq after DNA contamination removal,  table of RPKM values for low input RNA-Seq reads after DNA contamination removal

source_name: sorted spleen-resident macrophages

extract_protocol:
low-input RNA-Seq
Tissues were dissected from 10 mice. Spleen, brain, visceral fat and subcutaneous fat were excised and digested for 30 minutes with collagenase (Sigma) at 37oC with shaking. Sympathetic nerve fibers were isolated from subcutaneous adipose tissues and digested for 30 minutes with Hyaluronidase (Sigma) at 37oC with shaking, washed and further digested with collagenase for 15 minutes. SCG were dissected and digested with collagenase for 10 minutes, washed and further digested with trypsin (Biowest) for 30 minutes at 37oC with shaking. Cell suspensions were filtered through a 70 mm sieve and centrifuged at 450 xg for 10 minutes.

value: spleen-resident macrophages

tag: time in culture

value: ex vivo


title: vATM_ND_rep1

source_name: sorted anti-inflammatory white adipose tissue (WAT) macrophages (ATM) from fat visceral (vATM)

value: anti-inflammatory white adipose tissue (WAT) macrophages (ATM) from visceral fat


title: vATM_ND_rep2


title: MRS772

value: no


title: input_WT MeDIP-seq


title: SpM_ND_rep2


title: SpM_ND_rep1


title: SAM_ganglia_ND_rep3

source_name: sorted sympathetic-associated macrophages ganglia


title: sATM_ND_rep1

source_name: sorted anti-inflammatory white adipose tissue (WAT) macrophages (ATM) from subcutaneous fat (sATM)


title: SAM_ganglia_ND_rep1


title: SAM_fibers_ND_rep2

source_name: sorted sympathetic-associated macrophages fibers


title: Srap1 KO_ mouse ES_RNA-seq_R2

data_processing:
For RNA-seq, ChIP-seq and DIP-seq, raw reads were trimmed to remove adapters and low-quality reads using Trim Galore (v0.3.5).
Bowtie (v0.12.8) was used to obtain reads mapped uniquely to the mouse genome (mm9). ChIP and DIP peak candidates were identified with MACS (v2.1.1)using input as the control data set.
For RNA-seq, Cufflinks (v 2.2.1.0) was used to assemble transcripts, estimate their abundances and test for differential transcript expression.
Genome_build: mm9

value: embryonic stem cells (ES cells)

value: rRNA-depleted RNA


title: SAM_ganglia_ND_rep2


title: SAM_fibers_ND_rep1


title: Microglia_ND_rep3

value: microglia


title: Microglia_ND_rep1


title: Microglia_ND_rep2


title: MRS764

value: yes


title: BB1

tag: female genotype

value: Beijing

tag: genotype of male the female mated with

tag: replicate


title: U2-R

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.8
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1  was used to generate bigwig files
Genome_build: Ensembl; GRCh38
Supplementary_files_format_and_content: AltAnalyze 2.0.8 was used to generated a table of RPKM values

source_name: fibroblasts

growth_protocol: hiPSCs and hESCs were grown in E8 media on  Matrigel

extract_protocol:
RNA-seq:mRNA was extracted using the miRNEASY kit from Qiagen ChIP-seq:Cells were crosslinked with formalin
RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep

treatment_protocol: no treatment

value: human induced pluripotent stem cells (hiPSCs)

tag: passages

tag: reprogramming method

value: microRNA

tag: clone


title: U2K4-C

value: H3K4me3 (Active Motif, 39159)


title: U1K4-C


title: U2K27

value: H3K27me3 (Active Motif, 39155)


title: U2HDAC2-C

value: HDAC2 (Cell Signaling, 2545S)


title: U1-R


title: U1HDAC2-C


title: U1H3

value: H3 (Active Motif, 61475)


title: sATM_ND_rep2

value: anti-inflammatory white adipose tissue (WAT) macrophages (ATM) from subcutaneous fat


title: S2-R

value: Sendai Virus


title: S2H3


title: S2HDAC2-C


title: S1K4-C


title: U2H3


title: U1K27


title: S2K4-C


title: S2K27


title: S1K27


title: M2H3

value: mRNA


title: S1H3


title: M1-R


title: M2K27


title: M2K4-C


title: M2-R


title: 273p10NaB

description: NaB.txt

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.8
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1  was used to generate bigwig files
Genome_build: GRCh38
Supplementary_files_format_and_content: AltAnalyze 2.0.8 was used to generated a table of RPKM values

source_name: PBMCs

extract_protocol:
RNA-seq:mRNA was extracted using the miRNEASY kit from Qiagen ChIP-seq:Cells were crosslinked with formalin
RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina ChIP-seq:   NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep RNA-seq2: 1. mRNA enriched using oligo(dT) beads, 2. fragmented using fragmentation buffer, 3. cDNA synthesis using random hexamer, 4. adapter ligation, 5. Illumina Hiseq 4000 2x150

value: hiPSCs

tag: treatment

value: 0.2 mM Sodium Butyrate


title: M1k4-C


title: M1K27


title: S1HDAC2-C


title: 273p10DMSO

description: NaB.txt

value: DMSO


title: 274p10NaB

description: NaB.txt


title: Lentip10NaB

description: NaB.txt

value: LentiVirus


title: 274p10DMSO

description: NaB.txt


title: M1H3


title: Lentip10DMSO

description: NaB.txt


title: M1HDAC2


title: mNET-seq_Raji-CDK9as_1NA-PP1_rep2

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

institute: MPI

description:
Human Black, Burkitt′s lymphoma
Pol II-associated RNA

data_processing:
Library strategy: mNET-seq
Sequencing data preprocessing. Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for each of the samples, i.e. mNET-seq samples with 1-NA-PP1 (CDK9as inhibitor) and with DMSO (control) treatment. Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin and Gingeras, 2015) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. Antisense bias (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) was determined using positions in regions without antisense annotation with a coverage of at least 100 according to Refseq annotated genes (UCSC RefSeq GRCh38). mNET-seq coverage tracks were size factor normalized on 260 TUs that showed a response of less than 5% in the TT-seq signal upon 1-NA-PP1 (CDK9as inhibitor) treatment. The response ratio was determined as described above including also TUs with multiple TSS to extend the number of TUs for normalization. Note that variation of the response ratio cutoff and thereby the number of TUs available for normalization does virtually not change the normalization parameters. Coverage tracks for further analysis were restricted to the last nucleotide incorporated by the polymerase in the aligned mNET-seq reads.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

source_name: Raji B lymphocyte cells (CDK9as)

growth_protocol: Raji B cells were obtained from DSMZ (DSMZ no.: ACC 319) and grown in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA USA) supplemented with 10 % foetal calf serum (bio-sell, Nürnberg ,Germany), 100 U/mL penicillin and 100 µg/mL streptomycin (Thermo Fisher Scientific, Waltham, MA USA), and 2 mM L-glutamine (Thermo Fisher Scientific, Waltham, MA USA) at 37 °C and 5% CO2. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, San Diego, CA USA).

extract_protocol:
mNET-seq (Nojima et al., 2016; Schlackow et al., 2017)
TruSeq Small RNA Library (Illumina)

treatment_protocol: Cells were treated for 15 minutes with 0.05 % v/v solvent DMSO (Sigma) or 5 µM of 1-NA-PP1 (CDK9as inhibitor) (Calbiochem, EMD Millipore).

tag: cell line

value: Raji

value: B lymphocyte cells

tag: genotype

tag: method protocol

tag: antibody

value: MABI0601 (BIOZOL)

tag: treatment conditions

value: 15 min of 5 µM of 1-NA-PP1 (CDK9as inhibitor) (Calbiochem, EMD Millipore).


title: LSJ2HDAC2

source_name: hESCs

tag: cell type

value: human embryonic stem cells (hESCs)

tag: chip antibody


title: LSJ2-R


title: LSJ2H3


title: S1-R

value: human induced pluripotent stem cells (hiPSCs)


title: mNET-seq_Raji-CDK9as_1NA-PP1_rep1b

value: mNET-seq (Nojima et al., 2016; Schlackow et al., 2017)


title: LSJ2K27

value: H3K27me3 (Active Motif, 39155)


title: mNET-seq_Raji-CDK9as_DMSO_rep2

value: 15 minutes with 0.05 % v/v solvent DMSO (Sigma).


title: LSJ1HAC2

value: HDAC2 (Cell Signaling, 2545S)


title: LSJ1K27


title: mNET-seq_Raji-CDK9as_DMSO_rep1b


title: mNET-seq_Raji-CDK9as_1NA-PP1_rep1a


title: LSJ1H3

value: H3 (Active Motif, 61475)


title: L2-R


title: M2HDAC2


title: L2k4-C

value: H3K4me3 (Active Motif, 39159)


title: TT-seq_Raji-wt_1NA-PP1_rep2

description:
Human Black, Burkitt′s lymphoma
4sU-labeled RNA

data_processing:
Library strategy: TT-seq
Sequencing data preprocessing. Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for each of the samples, i.e. 2 replicates of TT-Seq with 1-NA-PP1 treatment and 2 replicates of TT-Seq with DMSO treatment. Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
We used a spike-in (RNAs) normalization strategy essentially as described before in (Schwalb et al., 2016) to allow observation of global shifts and antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015). Sequencing depth calculations resulted in no detectable global differences.
Calculation of the number of transcribed bases (coverage). For each sample aligned duplicated fragments were discarded. Of the resulting unique fragment isoforms only those were kept that exhibited a positive inner mate distance. The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38, ~ 98% of all fragments) in addition to the sum of the coverage of non-evident fragment parts (entire fragment).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

source_name: Raji B lymphocyte cells (wild type)

extract_protocol:
TT-seq (Schwalb et al., 2016)
Ovation Universal RNA-Seq System (NuGEN)

value: wild type

value: TT-seq (Schwalb et al., 2016)

value: 15 min of 5 µM of 1-NA-PP1 (CDK9as inhibitor) (Calbiochem, EMD Millipore); incl. 4sU-labeling during the last 5 minutes.


title: TT-seq_Raji-wt_DMSO_rep1

value: 15 minutes with 0.05 % v/v solvent DMSO (Sigma); incl. 4sU-labeling during the last 5 minutes.


title: TT-seq_Raji-wt_DMSO_rep2


title: TT-seq_Raji-wt_1NA-PP1_rep1


title: L2HDAC2-C

value: LentiVirus


title: L1-R


title: L2K27


title: APIPC_P_CSR1_B

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: LNCaP-shAR/pATK  human prostate tumor cell line cultured in 5% CSS + 1nM R1881 for 24 hrs

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.64.0 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Sequencing reads were mapped to the hg19 human genome using TopHat v2
Mean and standard deviation of fragment size were calculated with picard-tools v2.7.1
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package v1.0.1.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are tab delimited text files. Each file contains 7 columns: Entrez gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped)

extract_protocol:
RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol.  On-column DNase digestion was performed.  RNA concentration, purity, and integrity was assessed by NanoDrop (Thermo Fisher Scientific Inc) and Agilent Bioanalyzer.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

treatment_protocol: LNCaPshAR cells stably transfected with a tetracycline-inducible anti-AR shRNA, as previously described (Cheng et al., 2006), were obtained as a gift from Dr. Paul S. Rennie.  These cells were further modified via Lipofectamine 2000 (Invitrogen) transfection of a plasmid encoding a triple-probasin-driven herpes thymidine kinase (HSV-TK) and a Zeocin resistance cassette.  A clonal population of this cell line derived from Zeocin (Invitrogen) selection and serial dilution in a 96-well plate, which we refer to as LNCaPshAR/pATK, was subjected to total AR pathways suppression (TAPS): for two weeks the cells were grown in RPMI1640+5%CSS; at week 3, media was supplemented with 1mg/ml doxycycline.  Media was changed every 3-4 days and LNCaPshAR/pATK was maintained under TAPS for five months.  A surviving colony of proliferating cells emerged.  Following a 3-month expansion, this population of cells was treated with 50µM ganciclovir (GCV; InvivoGen) for two weeks to eliminate any cells still robustly expressing an AR transcriptional program.  We referred to the surviving population as LNCaPAPIPC.

tag: gender

value: male

value: prostate cancer

tag: cell culture media

value: pheno-red free RPMI-1640 + 5% CSS (Charcoal Dextran stripped FBS) (Gemini) + 1% PenStrep + 1nM R1881


title: APIPC_P_CS_B

description: LNCaP-shAR/pATK  human prostate tumor cell line cultured in 5% CSS for 24 hrs

value: pheno-red free RPMI-1640 + 5% CSS (Charcoal Dextran stripped FBS) (Gemini) + 1% PenStrep


title: APIPC_P_CSR1_A

source_name: LNCaP-shAR/pATK  human prostate tumor cell line


title: APIPC_P_CS_A

value: LNCaP-shAR/pATK  human prostate tumor cell line


title: L1K4-C

value: human induced pluripotent stem cells (hiPSCs)


title: LSJ1-R

value: human embryonic stem cells (hESCs)


title: APIPC_CSR1_B

description: LNCaP-APIPC human prostate tumor cell line cultured in 5% CSS + 1nM R1881 for 24 hrs


title: L1K27

value: H3K27me3 (Active Motif, 39155)


title: APIPC_CSR1_A

source_name: LNCaP-APIPC human prostate tumor cell line


title: mNET-seq_Raji-CDK9as_DMSO_rep1a

value: Raji

value: B lymphocyte cells

value: mNET-seq (Nojima et al., 2016; Schlackow et al., 2017)

value: MABI0601 (BIOZOL)

value: 15 minutes with 0.05 % v/v solvent DMSO (Sigma).


title: L1HDAC2-C

value: HDAC2 (Cell Signaling, 2545S)


title: APIPC_CS_C

description: LNCaP-APIPC human prostate tumor cell line cultured in 5% CSS for 24 hrs


title: L1H3

value: H3 (Active Motif, 61475)


title: J1K4

value: H3K4me3 (Active Motif, 39159)


title: APIPC_CS_B

value: LNCaP-APIPC human prostate tumor cell line


title: HUES9-R


title: J2K4


title: HUESK4


title: HUESHDAC2


title: H9-R


title: HUES9K27


title: HUES9H3


title: H9K27


title: H9K4


title: H9HDAC2


title: H9H3


title: TP17 96 h Gonadotropin Treatment Illumina RNASeq

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Sequence reads were trimmed using Cutadapt v 1.9.1 (adapter and qual 13)
Reads of each sample were aligned to reference using Tophat v 2.1.1 associated with Bowtie v 2.2.8
Mapped Reads of each sample were assembled into transcripts using Cufflinks v 2.2.1 with reference guided approach and masking rRNA, tRNA and small RNA (length < 200 bp)
Assembled transcripts of each sample were merged into a single Cuffmerge assembly using a reference guided approach. Reference annotation without rRNA, tRNA, small RNA (length < 200 bp) and LOC106997702 gene was used
Read counts on the cuffmerge assembled genes were obtained using HTSeq v 0.6.1p1
Genes of the samples were filtered (raw CPM > 1 for any 3 samples), library normalized (TMM), expression values as normalized CPM calculated and differential expression analyzed (exactTest) using edgeR
Genome_build: rheMac8

organism: Macaca mulatta

source_name: testis

extract_protocol:
The right testis from each animal was rapidly divided into 10 fragments and snap-frozen in liquid nitrogen and stored at -80C until RNA extraction.  Total RNA was isolated from the testes using Trizol reagent. TruSeq Stranded Total RNA library preparation was performed using 1ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pulsatile gonadotropin (FSH+LH)/vehicle infusion was performed for 48 or 96 h

tag: tissue

value: testis

tag: age

value: 14 months

value: wild type


title: TP18 96 h Gonadotropin Treatment Illumina RNASeq


title: TP12 48 h Gonadotropin Treatment Illumina RNASeq

value: 15 months


title: H7HDAC2-C


title: TP16 96 h Gonadotropin Treatment Illumina RNASeq


title: H7K27


title: TP15 96 h Gonadotropin Treatment Illumina RNASeq


title: TP08 48 h Gonadotropin Treatment Illumina RNASeq

value: 22 months


title: H7H3


title: TP09 Vehicle Treatment Illumina RNASeq


title: TP10 48 h Gonadotropin Treatment Illumina RNASeq


title: ES02K4


title: ES02-R


title: H7-1-R


title: Fib2-R

value: fibroblasts


title: H7K4

value: human embryonic stem cells (hESCs)


title: ES02HDAC2


title: E2K4-C

value: human induced pluripotent stem cells (hiPSCs)

value: Episomal


title: E2H3


title: TP07 Vehicle Treatment Illumina RNASeq

value: 24 months


title: E1-R


title: Fib1-R


title: ES02H3


title: E2-R


title: E2K27

value: H3K27me3 (Active Motif, 39155)


title: ES02K27


title: E1K4-C


title: TP11 Vehicle Treatment Illumina RNASeq


title: E2HDAC2-C


title: E1HDAC2


title: tps_Tre_9

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.1.2 was used to map reads to the WS210  version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR exact test was used on normalized count tables for differential expression analysis. Genes with counts per million (CPM) >1 in at least 4 libraries were included in the analysis.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries).

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Strains were grown on OP50 plates at 20C, and adults were hypochlorite treated to obtain embryos.

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit. 500ng of starting RNA was used and 12 cycles of PCR were used to amplify libraries.

treatment_protocol: Embryos were grown in S-basal (with or without 50mM trehalose) at a density of 1 embryo/uL. After 24 hours, L1 larvae were spun down and flash frozen in liquid nitrogen and stored at -80C until RNA extraction.

tag: strain

value: tps-1;tps-2 double mutant

tag: buffer

value: 50mM trehalose in S-basal

tag: developmental stage

value: L1 larvae


title: tps_Tre_3


title: TT-seq_Raji-CDK9as_1NAPP1_rep1

data_processing:
Sequencing data preprocessing. Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for each of the samples, i.e. 2 replicates of TT-Seq with 1-NA-PP1 treatment and 2 replicates of TT-Seq with DMSO treatment. Reads were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
We used a spike-in (RNAs) normalization strategy essentially as described before in (Schwalb et al., 2016) to allow observation of global shifts and antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015). Sequencing depth calculations resulted in no detectable global differences.
Calculation of the number of transcribed bases (coverage). For each sample aligned duplicated fragments were discarded. Of the resulting unique fragment isoforms only those were kept that exhibited a positive inner mate distance. The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38, ~ 98% of all fragments) in addition to the sum of the coverage of non-evident fragment parts (entire fragment).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig files containing the coverage

growth_protocol: Raji B cells were grown in RPMI 1640 medium (Gibco) supplemented with 10 % foetal calf serum (bio-sell), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), and 2 mM L-glutamine (Gibco) at 37 °C and 5 % CO2. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen).

extract_protocol:
Cells were harvested by centrifugation at 3,000 x g for 2 min. Total RNA was extracted using QIAzol according to the manufacturer’s instructions. RNAs were sonicated to generate fragments of <1.5 kb using AFAmicro tubes in a S220 Focused-ultrasonicator (Covaris). 4sU-labeled RNA was purified from 150 µg total fragmented RNA. Separation of labeled RNA was performed using streptavidin beads (Miltenyi Biotec). Prior to library preparation, 4sU-labeled RNA was purified and quantified. Enrichment of 4sU-labeled RNA was analyzed by RT-qPCR as described before in (Schwalb et al., 2016). Input RNA was treated with HL-dsDNase (ArcticZymes) and used for strand-specific library preparation according to the Ovation Universal RNA-Seq System (NuGEN). The size-selected and pre-amplified fragments were analyzed on a Fragment Analyzer before clustering and sequencing on the Illumina HiSeq 1500.
NuGEN Ovation Universal RNA-Seq System, starting with 100 ng RNA input

treatment_protocol: Reactions including RNA spike-ins were performed essentially as described before in (Schwalb et al., 2016). Two independent biological replicates were prepared for the present study. Briefly, for TT-seq experiments, 3.3 x 107 Raji B cells were treated for 15 minutes with solvent (DMSO) or 5 µM of 4-Amino-1-tert-butyl-3-(1ʹ-naphthyl)pyrazolo[3,4-d]pyrimidine (1-NA-PP1) (Calbiochem). Labeling was performed with the addition of 500 µM of 4-thiouracil (4sU) (Sigma) for 5 min at 37 °C and 5 % CO2.

value: 15 min of 5 µM of 1-NA-PP1 (CDK9as inhibitor) (Calbiochem, EMD Millipore); incl. 4sU-labeling during the last 5 minutes.

value: B lymphocyte cells

value: TT-seq (Schwalb et al., 2016)


title: tps_Tre_6


title: TT-seq_Raji-CDK9as_DMSO_rep1

value: 15 minutes with 0.05 % v/v solvent DMSO (Sigma); incl. 4sU-labeling during the last 5 minutes.


title: TT-seq_Raji-CDK9as_DMSO rep2


title: E1H3

tag: passages

tag: reprogramming method

value: H3 (Active Motif, 61475)


title: tps_Sba_8

value: S-basal


title: C2-R

value: Minicircle

tag: clone


title: tps_Sba_3


title: tps_Sba_6


title: tps_Sba_9


title: C2K27


title: C2HDAC2

value: HDAC2 (Cell Signaling, 2545S)


title: C2K4-C

value: H3K4me3 (Active Motif, 39159)


title: N2_Tre_9


title: C2H3


title: N2_Tre_6